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Section 2. Medbiosciences
https://doi.org/10.29013/ELBLS-20-2.3-7-31
An Isabella,
Union County Academy for Allied Health Sciences, Scotch Plains, New Jersey, USA, E-mail: [email protected]
A SYSTEMATIC ANALYSIS OF SLC9A9 SNP SITES AND THEIR ASSOCIATION WITH HUMAN DISEASE
Astract
Attention deficit-hyperactivity disorder (ADHD) is a children's disorder with inattention and hyperactive-impulsive behavior. Recent studies have shown several single-nucleotide polymorphisms (SNPs) of the gene SLC9A9, which encodes for an endosomal sodium/hydrogen ion transporter protein, are genetically associated with ADHD. However, the underlying mechanism and association between these SNP sites and ADHD still remain unknown. In this study, a systematic analysis and annotation of all SLC9A9's SNP sites in human populations were made, then disease-associated SNPs were identified, and finally, ADHD- or ASD-related SNPs were focused on for functional investigation. In total, there are 105,334 SNPs in the SLC9A9 gene locus. The majority of these sites are located in the intron region. There are 725 exonic SNPs including 208 SNPs that encode synonymous amino acids. Among the SNPs that can influence the primary protein sequence of SLC9A9, 41 SNPs were identified as mutant sites in various human cancers. Only two exonic missense variations, rs1248614031 and rs121912597, are associated with ADHD (rs1248614031) and ASD (rs121912597). Both sites are located in the functional cation/H+ exchanger domain of SLC9A9 protein. The former causes a change in the 409th amino acid residue from alanine to proline (A409P), while the latter leads to premature termination of protein translation (R423X). Mechanism study revealed that A409P is not found to be significant in maintaining protein structure, function, or stability. It does not affect active site binding, and likely not stability, but is likely associated with mediating protein-protein interactions that regulate SLC9A9 function.
Keywords: Attention Deficit-Hyperactivity Disorder (ADHD), Autism Spectrum Disorder (ASD), SLC9A9, Single-Nucleotide Polymorphisms (SNPs).
1. Introduction
Attention deficit-hyperactivity disorder (ADHD) is a children's disorder with inattention and hyperactive-impulsive behavior. It is a neurological disorder that affects children, but symptoms may persist into adulthood. Individuals suffering from this disorder exhibit hyperactivity, inatten-
tion, impulsivity, and problems in social interaction and academic performance. Recent literature published about ADHD and other neurological diseases relate ADHD-like symptoms in children to autism spectrum disorder (ASD) and reveal a high phenotypical overlap between ASD and ADHD [1]. Studies find that autism spectrum disorder
(ASD) and attention-deficit/hyperactivity disorder (ADHD) are often comorbid. Three distinct pathways between ASD and ADHD were identified: (1) from impulsivity to difficulties with understanding social information, (2) from hyperactivity to stereotypic, repetitive behavior, (3) a pairwise pathway between inattention, difficulties with understanding social information, and verbal IQ. ASD has profound etiological and clinical heterogeneity, which has impeded the identification of risk factors and pathophysiological processes underlying the disorder. A constellation of (i) types of genetic variation, (ii) modes of inheritance and (iii) specific genomic loci and genes have all recently been implicated in ASD risk, and these findings are currently being extended with functional analyses in model organisms and genotype-phenotype correlation studies. The overlap of risk loci between ASD and other NDDs (including ADHD) raises intriguing questions around the mechanisms of risk [2].
ADHD is a neurological disease mainly affecting the prefrontal cortex, a portion of the brain responsible for controlling goal-directed behavior, which involves multiple sensory, motor, and cognitive processes. When engaged in a task, the animal must attend to task-relevant sensory cues, control the initiation and termination of appropriate motor actions, and monitor the outcome of each action in order to adjust future behavioral strategies. ADHD symptoms include a decrease in recognition of sensory cues, inability to control initiation and termination of appropriate motor actions, and incomplete or incorrect adjustment of future behavioral strategies based on outcomes of an action [3]. Other areas of the brain affected are the dorsal striatum and hippocampus.
SLC9A9 (solute carrier family 9, member 9, also known as Na+/H+ exchanger member (NHE9)) is a membrane protein that regulates the luminal pH of the recycling endosome, an essential organelle for synaptic transmission and plasticity. Recent studies have shown several single-nucleotide polymorphisms (SNPs) of the gene are genetically associated
with ASD and ADHD. However, the underlying mechanism and association between these SNP sites and ADHD still remain unknown. This study aims to provide a systematic analysis of SLC9A9's SNP sites and their relation to human diseases, specifically ADHD, and find important SNP sites to extensively research and discuss the underlying mechanism between these sites and ASD and ADHD.
2. Materials and methods
Publically available databases and tools were mainly used to complete this study. First, an SNP database was used for SLC9A9 to curate a comprehensive list of SNP sites. Next, these sites were further performed genomic and exonic annotation, and disease association was also analyzed after function annotation to identify those SNP sites associated with ASD and/or ADHD. Once exonic SNP sites were determined to have association with ASD or ADHD, further functional and mechanism analysis was completed including an in-depth examination of effects on protein structure, protein interaction, active site function (small molecule binding, modification, etc.), topology, stability, gene expression level (from GTEX data sets), etc.
Databases and tools used in the study are shown as follows: dbSNP (https://www.ncbi.nlm.nih. gov/snp/), cBioPortal (http://www.cbioportal. org/), wANNOVAR (http://wannovar.wglab. org/), ClinVar (https://www.ncbi.nlm.nih.gov/clin-var/), InterPro (https://www.ebi.ac.uk/interpro/), UniProt (http://www.uniprot.org/), STRING (https://string-db.org). BioGRID (https://thebi-ogrid.org), COSMIC (https://cancer.sanger.ac.uk/ cosmic/), TCGA (https://portal.gdc.cancer.gov/), GTEx (https://gtexportal.org/), and so on. The general workflow in the current study is shown in
(Figure 1).
All SNPs of SLC9A9 were probed mainly through the dbSNP database and annotated using the wANNOVAR tool, such as annotation for disease association. Exonic SNPs with encoded amino acid change were paid more attention for function and disease
mechanism analyses. Serval aspects, including pro- protein stability and gene expression, were taken into tein structure, protein-protein interaction (PPT), consideration using their corresponding databases conservative active site, transmembrane topology, or tools for functional analyses.
Figure 1. Work flow in the current analysis
3. Results
3.1 Identifying SNP sites of human SLC9A9 gene
Furthermore, an extensive overview of existing literature on the topic of SLC9A9 SNPs/mutations associated with ASD and/or ADHD was conducted, and novel SNPs were considered in the study to be reviewed. SLC9A9 was first identified to be the gene of interest for this study as it is associated with a wide variety of human diseases, including cancer, etc. The human gene SLC9A9 encodes solute carrier family 9
member A9 (SLC9A9) which is also known as sodium hydrogen exchanger 9 (NHE9). In the past decade, increasing amounts ofliterature on SLC9A9 and its association with neurological disorders has been noted, indicating it is a relatively new and rapidly growing area of study for genetics associated with neurological health and disease. Within the past two years, three or more studies for SLC9A9 mutations associated with ASD and/or ADHD have been published, a strong indicator that it is a gene worth studying.
Figure 2. Functional distribution of 725 exonic SNPs
After selecting SLC9A9 as the gene of study, SNP databases were browsed and analyzed for all SNP sites associated with human disease. Altogether, a database of 105,334 SNPs in the SLC9A9 gene locus was compiled from dbSNP. The result file including all of the SNP sites was converted to VCF (Variant Call Format) format and run through wANNOVAR, which completed a SNP site annotation for all SNP sites. The genome wide SNP site annotation found a maj ority of SNP sites to be located in the intron region; however, this study focused more on SNPs in exons because of the potential change of amino acid residues. wANNOVAR also provided an exonic annotation of SNP sites and using database analysis methods, ClinVar significant SNP sites were identified.
In total, there were 725 exonic SNPs, and most of the exonic SNPs belong to nonsynonymous SNPs, with only 208 SNPs encoding synonymous amino acids (Table 1, Figure 2), suggesting that potential disease SNP sites could be identified among these sites. For example, there were 49 SNPs that have also been identified as mutant sites in various cancers, suggesting important roles of these sites in human cancer development. About 46% of the exonic SNPs were located in the functional cation/H+ exchanger domain of SLC9A9 protein.
3.2 Disease association analysis for SLC9A9's SNPs
The gene SLC9A9 is located on chromosome 3 (position 142,984,064-143,567,373 in human hg19 genome version) and is ubiquitously expressed in several tissues. SLC9A9 is responsible for the transport of sodium and hydrogen protons across cell membranes, including endosomal compartments which are where the protein is found most often. In the NCBI Nucleotide Database, SLC9A9 (or Homo sapiens solute carrier family 9 member A9) is found to be heavily associated with cancers in numerous tissues, as well as several different neurological disorders including autism spectrum disorder, epilepsy, and attention-deficit hyperactivity disorder. The NCBI Gene Database reveals SLC9A9 (solute car-
rier family 9 member A9 [Homo sapiens (human)] gene) is a protein encoding gene that encodes for a sodium/proton exchanger localized to late recycling endosomes in the cell and plays an important role in maintaining cation homeostasis.
A search of TCGA (The Cancer Genome Atlas) database revealed there were a total of 241 somatic mutations in the exons of SLC9A9 among all of 33 human cancers. Interestingly, after mutation annotation analysis using wANNOVAR revealed there were 49 SNPs that potentially could function as mutant sites in human cancers based on COSMIC (Catalogue of Somatic Mutations in Cancer) mutation database (Table 2). Among these sites, 16 missense mutations were also shared in the TCGA data sets. Therefore, these SNPs are suggested to be potentially associated with cancerous development but the cancerous function and detailed mechanism still awaiting further investigation.
Besides cancerous mutation association analysis, GWAS (Genome-wide association study) data were also investigated to find any possible association with other human diseases. The SLC9A9 gene is found in the cytogenetic region 3q24, has 23 associations, 20 studies, and 20 associated traits. Out of the 23 associations (Table 3), one association links SLC9A9 SNP to the attention-deficit hyperactivity disorder trait. This study was reviewed and the SNP site discussed (rs9810857) was found to be pheno-typically analyzed only. Since this study was focused on genotypically analyzed SNP sites, this SNP was not discussed and researched further.
In the ClinVar analysis summary of the exonic SNP sites related to human disease, only one was identified as related to ASD. This SNP was rs121912597, also known as R423X, and it is a stopgain mutation that leads to premature termination of protein translation. However, in an overview ofrecent literature published, another exonic missense variation (rs1248614031) was discovered to be associated with ADHD; although not yet reported in ClinVar, the SNP site was chosen for further analysis to determine its potential
effects on the SLC9A9 protein function. We focused on these two SNPs for further study.
PhyreRisk also provided variant analysis and predictions. rs1248614031 (A409P) had a PolyPhen prediction ofprobably damaging and a SIFT prediction of deleterious (Table 2). rs121912597 (R423X) did not have a Polyphen prediction or SIFT prediction (Table 2).
rs121912597 was associated with ASD in most protein structure and function databases. In NCBI Nucleotide, Protein, and Gene Databases, InterPro, UniProt, Reactome, and Phosphosite, rs121912597 and its related literature are cited as associated with susceptibility with autism. Reactome database provides a pathway analysis of the effect of R423X on the pathway function of SLC9A9. Rs1248614031 was not mentioned in any databases other than NCBI Protein and Gene Databases, in which it is cited in literature as being associated with ADHD. SNP databases were analyzed for more in depth classifications of rs121912597 and rs1248614031. db-SNP reported rs1248614031 as a single nucleotide variant on chr3: 143493743 (GRCh38.p12). It did not have a clinical significance reported in ClinVar, but the reason probably is update not in time.
The associated literature ascertains rs121912597 as a risk factor for autism spectrum disorder in a family of 2 male siblings and a mother. The 2 male siblings had autism spectrum disorder, one with epilepsy, and the mother had speech-language difficulties as a child. Morrow et al. (2008) identified a heterozygous nonsense mutation in the SLC9A9 gene (R423X; 608369.0001) in all three persons of study, indicating a heritable mutation and genetic risk factor for ASD (this information was obtained from OMIM databases). This literature is verified and meets criteria as evidence for R423X being linked to ASD, but there is no verified or updated literature found in dbSNP supporting an experimentally determined linkage between R423X and loss or alteration of function of SLC9A9, which would be linked to ASD and/or ADHD.
3.3 Functional mechanism analysis for disease SNPs of SLC9A9
SLC9A9 is part of the sodium proton exchangers (NHEs) and is an integral membrane protein transporter that counter-transports protons and sodium ions across lipid bilayers. In mammals in general, they are responsible for regulating cell pH, volume, and intracellular sodium concentration, while human NHEs also take part in cell growth of differentiation. The transport of protons out of the cell and sodium ions into the cell eliminates excess acid from actively metabolising cells. In mammals, NHE activity is found in most membranes of cells and cell organelles. There are nine isoforms identified in mammalian cells, and contain 10-12 membrane spanning regions at the N terminus and a large cytoplasmic region at the C terminus. Transmembrane regions M3-M12 are similar in identity with other members of the family, and M6 and M7 regions are greatly conserved in structure across all isoforms. This is considered the region that is involved in transporting sodium and hydrogen ions. Na+/H+ exchanger isoform 9 (SLC9A9) is located in the membranes of late recycling endosomes. SL-C9A9 is involved in the effusion of Golgi luminal H+ in exchange for cytosolic cations, and in maintaining organelle ion homeostasis by helping to maintain unique acidic pH values of the Golgi and endosomal compartments of the cell.
SLC9A9 is ubiquitously expressed in all tissues at RNA level that have been tested, but it is expressed at highest levels in heart and skeletal muscle, followed by placenta, kidney, and liver and in the brain, medulla and spinal cord. The Human Protein Atlas provided a summary of SLC9A9 RNA and protein expression in various tissues. In the brain tissue, SL-C9A9 RNA expression was highest in the spinal cord and lowest expression in the cerebellum. However, the cerebral cortex, hippocampal formation, and cerebellum had the highest expression of SLC9A9 at protein level, mostly in neuronal, endothelial, and purkinje cells.
As mentioned above that SLC9A9 has numerous exonic SNPs. To investigate the influence of these SNPs on protein functions, we selected two SNP sites, rs1248614031 and rs121912597, which are associated with ADHD (rs1248614031, A409P) and ASD (rs121912597, R423X). R423X is SLC9A9: NM_173653: exon11: c.C1267T: p.R423X, so it has a heterozygous C—>T transition in Exon 11. The literature provides a diagram of the position and consequences of the C^ T transition. wANNOVAR results confirm that the CGA^TGA change results in argi-nine residue at position 423 changing to a stop codon. The last diagram the literature provides is comparing the similarity in the nonsense mutations in the last extracellular loop of NHE proteins between SLC9A9 in patients with comorbid autism and epilepsy, and Nhe1 in the slow-wave epilepsy mouse. The SNV is considered rare as it was not found in greater than 3800 control chromosomes within this study.
We considered protein structure including transmembrane topology, protein interaction, active sites, protein stability and gene expression of SLC9A9 itself regulated by SNP to investigate functional mechanisms.
3.3.1 Protein structure
In order to further investigate molecular mechanisms on protein functions by nonsynonymous SNPs, particularly the ADHD and ASD associated SNPs, protein visualization databases and programs (SWISS-MODEL, ModBase, RSCB Protein Data Bank, and PhyreRisk) were used to visualize the loci, structure, and variants of SLC9A9. SWISS-MODEL repository data was searched and Q8IVB4's structure was modeled, including the transmembrane portion of the structure. The full length of SLC9A9 protein includes 645 amino acid residues. SLC9A9 contains 13 transmembrane helices and a conservative sodium/hydrogen exchanger domain that covers the 31486 aa (amino acids) (Figure 3). For rs1248614031 (A409P) and rs121912597 (R423X), both sites are located in the functional cation/H+ exchanger domain of SLC9A9 protein. The former causes a change in the 409th amino acid residue from alanine to proline (A409P), while the latter leads to premature termination ofprotein translation (R423X). In addition, both sites are located in the region between the 11th and 12th transmembrane helices.
Figure 3. Domain and topology of SLC9A9. A) SLC9A9 contains a sodium/hydrogen exchanger domain. B) SLC9A9 contains 13 transmembrane helices
RCSB PDB and PhyreRisk were used to visualize the protein sequence and 3D structure of SLC9A9 and the SNPs of interest: R423X and A409P. PhyreRisk databases were used to visualize SNP sites on the protein and predict effect on protein structure and/or function. Both SNP sites were visualized and rs1248614031 (A409P) had a PolyPhen prediction while rs121912597 (R423X) did not. At this stage, existing literature was also reviewed extensively to determine any more experimentally supported effects both SNPs had on protein structure and function. This portion of the study was conducted with caution, as many of the literature was new and relatively unsupported by large amounts of statistical data.
3.3.2 Protein interaction
After protein structure and function analysis, protein interaction was analyzed through data from protein interaction databases (STRING, BioGRID
and Protein Data Bank - Europe). BioGrid did not have any updated information on protein interactions not related to cancer, so it was not analyzed extensively. The major data gathered from this portion of the study was STRING and its associated literature. BioGrid and PDB databases are not updated to recent literature publications, but were still analyzed. rs1248614031 (A409P) was identified from existing literature prior to the study began, and STRING databases supported the article's findings. Proteins that interacted with SLC9A9 were identified from STRING databases, most commonly CHP1 and DOCK3 were associated with neurological disease (Figure 4). Further analysis of these proteins was also conducted. Gene co expression data was obtained from STRING as well, supporting high levels of CHP1 and DOCK3 interaction in cells of tissues in the body.
Figure 4. Interacted
PubMed extracts and articles provided substantial amount of data to support CHP1 and DOCK3 functions being compromised and/or altered in association with ASD and/or ADHD. Experimentally modeled SLC9A9 interactions with CHP1 and DOCK3 were not found in PDB databases, but NHE1 and CHP1
proteins of SLC9A9
interaction structures were parsed and strongly experimentally supported. Although no parsed structures of SLC9A9 interacting with CHP1 were found in any protein structure databases, parsed structures of NHE1, the isoform 1 of the NHE family, interacting with cofac-tor CHP1 has been modeled in PDB databases.
According to literature and databases such as In-terPro and MatrixDB, CHP1 or calcium-binding protein is involved in many different processes such as regulation of vesicular trafficking, plasma membrane Na(+)/H(+) exchanger and gene transcription. The main role it plays in relation to SLC9A9 is constitutive exocytic membrane traffic and plasma membrane Na(+)/H(+) exchange. It helps in cell pH regulation by controlling plasma membrane-type Na(+)/H(+) exchange activity and affects the pH sensitivity of SL-C9A1/NHE1 (and likely its isoforms) by increasing its sensitivity at acidic pH. It is required for the stabilization and localization of SLC9A1/NHE1 at the plasma membrane (and likely its isoforms).
Although many interactors are predicted, whether the amino acids A409 and R423 play a key role to mediate this interaction still need further investigation.
3.3.3 Active site
Next we explored whether the SNP sites of SL-C9A9, rs1248614031 (A409P) and rs121912597 (R423X), could represent active sites for the protein's function. Because the reference allele encodes an alanine (A409) or arginine (R423), it means these residues should not be phosphorylation sites that generally happen at serine, threonine and tyrosine. Therefore, phosphorylation prediction tools such as the NetPhos 3.1 server could not obtain any results.
Motif scanning means finding all known motifs that occur in a sequence. We used the tool Motif Scan (https://myhits.isb-sib.ch/cgi-bin/motif_scan) to identify any possible known motifs that could be affected by these two SNPs. Although many motif sites including amidation, glycosylation, phosphorylation, myristoylation and leucine zipper were found in the protein sequence, no sites were truly involved in the above two SNPs, suggesting amino acid alternation could have no affection on post-translational modifications.
In addition, R423X and A409P were analyzed for effects on active site binding and ligand structure and bonding. Active site binding and ligand structure and bonding data came primarily from recent existing
literature, so there was not much statistical data to support results.
3.3.4 Protein stability
Protein stability was analyzed mainly based on ubiquitination sites, PEST motifs and protease cleavage sites in proteins. UbPred (http://www.ubpred. org/) is a random forest-based predictor of potential ubiquitination sites in proteins. It was trained on a combined set of266 non-redundant experimentally verified ubiquitination sites available from large-scale proteomics studies. Because ubiquitination, together with sumoylation, generally occurs in lysine (K), it means both SNPs should not be involved in ubiquitination and sumoylation.
The tool epestfind (http://emboss.bioinformat-ics.nl/cgi-bin/emboss/epestfind) was used to identify PEST motifs as potential proteolytic cleavage sites, but no PEST motifs were identified.
3.3.5 Gene expression
Gene expression by SNP was analyzed as well by using GTEx database. Perusing GTEX datasets revealed no significant tissue sQTLs or eQTLs for either SNP site, but the database has not been updated to most recent findings. GTEX datasets did produce expression levels of SLC9A9 in various tissues of the body, confirming high expression levels in brain tissue.
4. Discussion
The findings of the study are supported by data gathered from genomic, proteomic, and other databases, as well as existing literature on the subject. Exonic missense variations of both rs1248614031 and rs121912597 were associated with ADHD (rs1248614031) and ASD (rs121912597), respectively. The former causes a change in the 409th amino acid residue from alanine to proline (A409P), while the latter leads to premature termination of protein translation (R423X). Both SNP sites were functionally annotated and protein mechanism analyzed.
We analyzed protein structure, protein-protein interaction, and protein stability, and so on, to investigate the potential molecular mechanism of these
two SNPs on the function of SLC9A9 (Figure 5). Protein interaction was analyzed through data from protein interaction databases (STRING, BioGRID and Protein Data Bank — Europe). BioGrid did not provide results pertaining to the two variants of interest or diseases of interest. PDB databases were not updated to recent literature findings, so it was only used to visualize SNP sites of interest. The major data gathered from this portion of the study was STRING and its associated literature. rs1248614031 (A409P) was identified from existing literature prior to the study began, and STRING databases supported the article's findings. Proteins that interacted with SLC9A9 were identified from STRING databases, most commonly networks with CHP1 and DOCK3 were associated with neurological disease.
Four recently published studies about genetic mutations associated with ASD and/or ADHD focused on SLC9A9's interaction network with CHP1 (calcineurin-homologous protein 1) and DOCK3 and alterations in these networks that affect cell function and increase pathogenicity, leading to association with ASD and/or ADHD. At least 75% of these articles also ascertain that R423X is a critical SNP in altering the interaction network of SLC9A9, CHP1, DOCK3, and other proteins, which is related to increased pathogenicity of cells in the hippocampus, prefrontal cortex, and other areas of the brain in which pathogenicity relates to neurological disease such as ASD and/or ADHD. The most recently published findings associated with A409P had not been updated into the database, but the article supported ASD and/or ADHD symptoms and disease associated with SLC9A9 and alterations in protein-protein interaction networks with CHP1 and other proteins.
Gene co expression data was obtained from STRING as well, supporting high levels ofCHP1 and DOCK3 interaction in cells of tissues in the body. Further analysis of CHP1 and DOCK3 proteins was also conducted. According to literature and databases such as InterPro and MatrixDB, CHP1 or calcium-binding protein is involved in many different processes such as
regulation of vesicular trafficking, plasma membrane Na(+)/H(+) exchanger and gene transcription. The main role it plays in relation to SLC9A9 is constitutive exocytic membrane traffic and plasma membrane Na(+)/H(+) exchange. It helps in cell pH regulation by controlling plasma membrane-type Na(+)/H(+) exchange activity and affects the pH sensitivity of SL-C9A1/NHE1 (and likely its isoforms) by increasing its sensitivity at acidic pH. It is required for the stabilization and localization of SLC9A1/NHE1 at the plasma membrane (and likely its isoforms).
At this stage, existing literature was also reviewed extensively to determine any more experimentally supported effects both SNPs had on protein structure and function. This portion of the study was conducted with caution, as many of the literature was new and relatively unsupported by large amounts of statistical data. Alterations in protein interaction networks of SLC9A9 is adequately supported by a substantial amount of literature. The main literature cited and verified on R423X does not discuss proteinprotein interactions, but it does phenotypically confirm the genetic variant as a risk factor for ASD [4]. They performed a mutational analysis of SLC9A9 in nonconsanguineous pedigrees with comorbid autism and epilepsy. The mutational analysis of SLC9A9 in an AGRE pedigree showed a nonsense variation (also compared to nonsense mutation in Nhe1 in slow-wave epilepsy mice). The 2 sons are included in the pedigree, both with autism but one with comorbid epilepsy; the mother is included but does not have autism and instead has a speech-language symptom often related to ASD. Both sons and the mother are revealed to have the nonsense variation.
Two reports show that mutations of SLC9A9 can affect the interaction of SLC9A9 with CHP1 [5,6]. This particular study used co-immunoprecipitation methods and Western blot to determine that the two mutations found in rats with inattentive ADHD caused CHP and SLC9A9 binding to increase by almost two-fold. Although these two variants are not this study's variants of interest, the data supports the
theory that mutations leading to altered protein interaction networks between SLC9A9 and CHP are
associated with ADHD symptoms and pathology in at least mice and possibly humans.
Figure 5. SLC9A9 protein subcellular localization (A), expression (B, C), structure (D) and molecular function (E).
A) SLC9A9 protein components and interactome within a subcellular membrane [8]. B) SLC9A9 RNA and protein expression in brain tissue, RNA expression and protein expression in various regions of the brain. C) SLC9A9 RNA and protein expression in various body tissues (Human Protein Atlas, https://www.proteinatlas.org/ ENSG00000181804-SLC9A9/tissue). D) SLC9A9 3D structure, missense variation rs1248614031 (A409P) is located on 3D structure (purple) (PhyreRisk Sequence Browser and 3D Structure Viewer, http://phyrerisk.bc.ic. ac.uk/variant-detail/Q8IVB4?position=409&alteration=P&original=A&otherInfo=null&variantColour=0xF F00FF&source=User%20defined%20protein%20variant). E) SLC9A9 molecular function in regulatingH+ and Na+/K+ ion concentration, maintaining the necessary pH of endosomal subcellular compartment [9]
The third article found in STRING databases supporting protein interaction networks of SLC9A9 and CHP and their implications for ASD and/or ADHD was a continuation of the previous study [7]. In this study, however, they examined SLC9A9 expression and relationship to 9 more genes (including CHP) that could directly or indirectly interact with the protein in the hippocampus of ADHD affected rats. As supported by gene coexpression graphs from STRING, many expression levels of these genes were significantly correlated, including CHP. This study also discussed age-dependent variations of ADHD and differences in SLC9A9 protein networks based on age. Two different types of rat models with different strains of ADHD had similar profiles in adolescence but different ones in adulthood. Both ADHD rat models were distinctly different from the control rat models in adolescence and adulthood.
SLC9A9-CHP interactions were important to intracellular Ca2+ signaling and protein phos-phorylation, which are crucial signaling pathways for many cellular functions but especially synaptic transmission and plasticity. So, although SLC9A9 is mainly credited for maintenance of endosomal pH and intracellular pH levels, its interaction network with CHP is crucial for other cell functions that can also affect neurons and other brain cell functions (such as synapse function). Heterozygous stop co-don mutation (R423X) is known to truncate the SLC9A9 protein (based on Identifying autism loci and genes by tracing recent shared ancestry. Morrow et al 2008) and remove the C-terminal of SLC9A9 in patients with autism and epilepsy. Although this SNP is referred to, the study is not able to conclude exactly what functions are affected by mutations that affect SLC9A9's C-terminal. From evidence gathered in literature thus far, it seems to be that SLC9A9 protein-protein interaction networks (and especially the C-terminals) is a mechanism that can be affected by changes in SLC9A9 gene sequences and can affect numerous pathways and functions in the cell.
Within these articles, R423X is the only SNP site to have substantial evidence supporting it as a mutation that results in loss of SLC9A9 function, especially in protein-protein networks involving the C-terminus (which it truncates). A recent study quantitatively analyzed the SLC9A9 interactome by co-immuno-precipitation methods and mass spectrometry in order to evaluate the functions of SLC9A9 and effects of disease-associated variants on protein-protein interactions. The study investigated 100 proteins known to interact with SLC9A9, including CHP and others, and enriched them in functional pathways for SLC9A9. They found that A409P (and ADHD-associated mutation) notably altered SLC9A9's interactions with a group of proteins important in caveolae-mediated endocytosis and other signaling pathways. The study also found evidence that R423X (ASD associated nonsense mutation) led to no-detectable amount of SLC9A9 and therefore overall loss of SLC9A9 functional networks.
5. Conclusion
In conclusion, although A409P occurs in the cation/H+ exchanger domain, it is not found to be significant in maintaining protein structure, function, or stability. It does not affect active site binding with ion transport, and likely not stability, although this should be determined by experimentation. A409P is therefore likely associated with mediating protein-protein interactions and pathways, especially with proteins regulating SLC9A9 function in different functional pathways including calcium ion transport and signaling pathways. As for R423X, it is found to be significant in maintaining protein structure and therefore protein function. It is a stop gain variant, so the original amino acid changes to a stop codon and therefore truncates the protein. This truncation results in loss of the C-terminus, a binding site for CHP and other proteins that are crucial for SLC9A9 mediated protein-protein interaction network function. SLC9A9 loses its function and SLC9A9 protein levels in cells decrease. Both A409P and R423X SNPs are clinically associ-
ated with altered protein-protein interactions and function of SLC9A9, which can be positively associated with cell pathogenicity, especially in the brain where SLC9A9 is ubiquitously expressed, and where endosomal functional pathways are especially important to neuronal cell health and function. A summary information is shown in Table 4.
Increased cell pathogenicity in the brain may be associated with certain neurodevelopmental diseases such as ADHD, ASD, etc. rs1248614031 is a rare missense mutation of the SLC9A9 gene that results in a change in amino acid residue at the 409th position from Alanine to Proline and does not have enough evidence to link it to disrupted function, structure, stability, etc. of SLC9A9. This means that while R423X has substantial amounts of evidence in loss of primary function of SLC9A9, its effects on other pathways of SLC9A9 have yet to be studied extensively and may be the reason why it is associated with ASD/ADHD symptoms and disease. Further
Table 1. - SLC9A9 exot
research must be conducted on A409P to confirm its effects on different pathways of SLC9A9 and investigate why these pathways are related to ASD/ADHD molecular mechanisms and pathophysiology.
Further research should also be conducted on endosomal system pathways and their relationship to neurological disorders, in order to determine important novel pathways that may be implicated in ASD/ ADHD and disrupted by SLC9A9 mutations. Thus far, this study's findings support the theory that endosomal system pathways, in particular regulation of luminal pH and primary endosomal functions (transport, signaling reception, etc.) and more specifically protein-protein mediated pathways are highly connected to disruption or damage to neuronal cell development, health, and function and therefore ASD/ ADHD cellular mechanisms and pathophysiology. More research should be conducted, experimentally and phenotypically, to confirm these results.
SNPs and various data
No. Chr Start Ref Alt ExonicFunc.ref Gene AAChange No. Chr Start Ref Alt ExonicFunc.ref Gene AAChange
1 2 3 4 5 6 7 8 9 10 11 12 13 14
1 3 142985547 A G synonymous N645N 364 3 143292940 G A synonymous A330A
2 3 142985548 T A nonsynonymous N645I 365 3 143292940 G T synonymous A330A
3 3 142985554 T A nonsynonymous Q643L 366 3 143292941 G A nonsynonymous A330V
4 3 142985555 G A stopgain Q643X 367 3 143292942 C T nonsynonymous A330T
5 3 142985559 T C synonymous Q641Q 368 3 143292946 C A nonsynonymous E328D
6 3 142985559 T G nonsynonymous Q641H 369 3 143292948 C T nonsynonymous E328K
7 3 142985560 T C nonsynonymous Q641R 370 3 143292949 G A synonymous A327A
8 3 142985569 G A nonsynonymous T638I 371 3 143292951 C T nonsynonymous A327T
9 3 142985571 T C synonymous Q637Q 372 3 143292952 A C synonymous S326S
10 3 142985579 G C nonsynonymous L635V 373 3 143292953 G A nonsynonymous S326F
11 3 142985580 C G nonsynonymous K634N 374 3 143292956 A G nonsynonymous L325P
12 3 142985580 C T synonymous K634K 375 3 143292958 G A synonymous F324F
13 3 142985589 A T stopgain Y631X 376 3 143292962 G A nonsynonymous A323V
14 3 142985590 T C nonsynonymous Y631C 377 3 143292963 C G nonsynonymous A323P
15 3 142985591 A G nonsynonymous Y631H 378 3 143292966 T C nonsynonymous S322G
16 3 142985593 C A nonsynonymous G630V 379 3 143292970 A C synonymous S320S
17 3 142985596 C T nonsynonymous G629E 380 3 143292971 G C nonsynonymous S320C
18 3 142985602 C T nonsynonymous G627D 381 3 143292980 A G nonsynonymous F317S
19 3 142985603 C T nonsynonymous G627S 382 3 143292981 A G nonsynonymous F317L
20 3 142985604 G A synonymous L626L 383 3 143292982 A C nonsynonymous F316L
21 3 142985604 G T synonymous L626L 384 3 143292987 G A synonymous L315L
22 3 142985607 G A synonymous D625D 385 3 143292990 C T nonsynonymous G314S
1 2 3 4 5 6 7 8 9 10 11 12 13 14
23 3 142985607 G T nonsynonymous D625E 386 3 143292991 G - frameshift deletion G314Afs*18
24 3 142985608 T G nonsynonymous D625A 387 3 143292991 G A synonymous T313T
25 3 142985613 C T synonymous E623E 388 3 143292991 G C synonymous T313T
26 3 142985616 A C stopgain Y622X 389 3 143292991 G T synonymous T313T
27 3 142985617 T C nonsynonymous Y622C 390 3 143292998 A G nonsynonymous L311P
28 3 142985630 T C nonsynonymous K618E 391 3 143293000 C T nonsynonymous M310I
29 3 142985633 C A nonsynonymous G617C 392 3 143293002 T C nonsynonymous M310V
30 3 142985633 C G nonsynonymous G617R 393 3 143293003 C T synonymous P309P
31 3 142985634 T C synonymous P616P 394 3 143293004 G A nonsynonymous P309L
32 3 142985635 G A nonsynonymous P616L 395 3 143293004 G T nonsynonymous P309Q
33 3 142985637 C T synonymous T615T 396 3 143293008 A G nonsynonymous F308L
34 3 142985638 G A nonsynonymous T615M 397 3 143293011 C T nonsynonymous E307K
35 3 142985641 - G frameshift insertion Q614Pfs*9 398 3 143293012 A G synonymous C306C
36 3 142985643 G A synonymous P613P 399 3 143293014 A G nonsynonymous C306R
37 3 142985652 T C synonymous K610K 400 3 143293017 G C nonsynonymous L305V
38 3 142985653 T A nonsynonymous K610I 401 3 143293020 T C nonsynonymous K304E
39 3 142985655 C T synonymous Q609Q 402 3 143293021 G A synonymous T303T
40 3 142985657 G C nonsynonymous Q609E 403 3 143293021 G C synonymous T303T
41 3 142985657 G T nonsynonymous Q609K 404 3 143293030 G T synonymous T300T
42 3 142985658 G A synonymous D608D 405 3 143293032 T G nonsynonymous T300P
43 3 142985661 C T synonymous L607L 406 3 143297434 G A nonsynonymous T296I
44 3 142985667 T - frameshift deletion G606Vfs*38 407 3 143297441 T C nonsynonymous I294V
45 3 142985672 T A nonsynonymous R604W 408 3 143297443 G T nonsynonymous A293D
46 3 142985673 T C synonymous A603A 409 3 143297444 C A nonsynonymous A293S
47 3 142985674 G T nonsynonymous A603E 410 3 143297448 C T synonymous A291A
48 3 142985675 C T nonsynonymous A603T 411 3 143297449 G A nonsynonymous A291V
49 3 142985681 G A nonsynonymous P601S 412 3 143297449 G T nonsynonymous A291E
50 3 142985685 G A synonymous C599C 413 3 143297454 C A synonymous G289G
51 3 142985691 T A synonymous S597S 414 3 143297456 C T nonsynonymous G289R
52 3 142985692 G A nonsynonymous S597L 415 3 143297458 A - frameshift deletion M288Rfs*11
53 3 142985693 A G nonsynonymous S597P 416 3 143297459 T C nonsynonymous M288V
54 3 142985700 T - frameshift deletion A595Pfs*10 417 3 143297460 T G synonymous A287A
55 3 142985702 - C frameshift insertion Q594A-fs*29 418 3 143297467 G A nonsynonymous S285L
56 3 142985708 G A stopgain Q592X 419 3 143297468 A T nonsynonymous S285T
57 3 142985711 A C nonsynonymous Y591D 420 3 143297469 G A synonymous G284G
58 3 142985716 A G nonsynonymous I589T 421 3 143297470 C T nonsynonymous G284D
59 3 142985717 T C nonsynonymous I589V 422 3 143297471 C T nonsynonymous G284S
60 3 142985718 G A synonymous A588A 423 3 143297472 A - frameshift deletion G284Afs*15
61 3 142985720 C G nonsynonymous A588P 424 3 143297474 C T nonsynonymous A283T
62 3 142985720 C T nonsynonymous A588T 425 3 143297475 G A synonymous F282F
63 3 142985721 T C synonymous L587L 426 3 143297476 A G nonsynonymous F282S
64 3 142985723 G A synonymous L587L 427 3 143297483 C T nonsynonymous G280R
65 3 142985724 T A nonsynonymous E586D 428 3 143297490 A G synonymous N277N
66 3 142985728 T C nonsynonymous D585G 429 3 143297492 T A nonsynonymous N277Y
1 2 3 4 5 6 7 8 9 10 11 12 13 14
67 3 142985729 C A nonsynonymous D585Y 430 3 143297493 C T synonymous G276G
68 3 142985729 C T nonsynonymous D585N 431 3 143297495 C T nonsynonymous G276R
69 3 142985730 C A nonsynonymous Q584H 432 3 143297497 A G nonsynonymous V275A
70 3 142985734 T C nonsynonymous N583S 433 3 143297499 A G synonymous S274S
71 3 142985735 T A nonsynonymous N583Y 434 3 143297501 A T nonsynonymous S274T
72 3 142985738 C A nonsynonymous V582L 435 3 143297505 G T nonsynonymous F272L
73 3 142985739 A G synonymous I581I 436 3 143297516 C A nonsynonymous A269S
74 3 142985740 A G nonsynonymous I581T 437 3 143297516 C T nonsynonymous A269T
75 3 142985744 A T nonsynonymous C580S 438 3 143297517 G A synonymous A268A
76 3 142985751 A G synonymous D577D 439 3 143297518 G C nonsynonymous A268G
77 3 142985753 C T nonsynonymous D577N 440 3 143297528 C T nonsynonymous A265T
78 3 142985757 CT - frameshift deletion E575Gfs*1 441 3 143297529 A G synonymous N264N
79 3 142985760 T G nonsynonymous K574N 442 3 143297531 T C nonsynonymous N264D
80 3 142985761 T C nonsynonymous K574R 443 3 143297534 G A nonsynonymous P263S
81 3 142985763 T C synonymous L573L 444 3 143297538 C G nonsynonymous E261D
82 3 142985765 G A synonymous L573L 445 3 143297548 C G nonsynonymous S258T
83 3 142985766 C T synonymous Q572Q 446 3 143297550 G A synonymous Y257Y
84 3 142985767 T G nonsynonymous Q572P 447 3 143297555 T C nonsynonymous I256V
85 3 142985771 C G nonsynonymous E571Q 448 3 143297561 T C nonsynonymous I254V
86 3 142987718 C T nonsynonymous G570E 449 3 143297562 A G synonymous S253S
87 3 142987719 C A nonsynonymous G570W 450 3 143371099 T C synonymous T251T
88 3 142987720 A G synonymous Y569Y 451 3 143371107 C T nonsynonymous V249I
89 3 142987721 T A nonsynonymous Y569F 452 3 143371110 T C nonsynonymous I248V
90 3 142987724 G T nonsynonymous A568D 453 3 143371113 C A nonsynonymous A247S
91 3 142987727 T C nonsynonymous Q567R 454 3 143371114 C T synonymous V246V
92 3 142987728 G A stopgain Q567X 455 3 143371115 A G nonsynonymous V246A
93 3 142987729 - G frameshift insertion Q567Sfs*10 456 3 143371119 C T nonsynonymous A245T
94 3 142987736 G A nonsynonymous T564I 457 3 143371129 C T synonymous V241V
95 3 142987740 G A nonsynonymous L563F 458 3 143371133 CT - frameshift deletion S240Cfs*3
96 3 142987750 A G synonymous I559I 459 3 143371138 T A synonymous G238G
97 3 142987751 A G nonsynonymous I559T 460 3 143371141 A G synonymous F237F
98 3 142987753 C T synonymous P558P 461 3 143371145 A G nonsynonymous L236S
99 3 142987754 G A nonsynonymous P558L 462 3 143371150 T C synonymous T234T
100 3 142987755 G A nonsynonymous P558S 463 3 143371150 T G synonymous T234T
101 3 142987757 C T nonsynonymous G557D 464 3 143371153 G A synonymous Y233Y
102 3 142987760 C T nonsynonymous C556Y 465 3 143371156 C G synonymous L232L
103 3 142987761 A G nonsynonymous C556R 466 3 143371164 G T nonsynonymous P230T
104 3 142987770 G A nonsynonymous P553S 467 3 143371167 C A nonsynonymous D229Y
105 3 142987774 TGT - nonframeshift deletion T551del 468 3 143371167 C T nonsynonymous D229N
106 3 142987779 T C nonsynonymous T550A 469 3 143371168 G A synonymous V228V
107 3 142987781 G C nonsynonymous T549S 470 3 143371170 C T nonsynonymous V228I
108 3 142987784 A T nonsynonymous L548Q 471 3 143371171 G A synonymous H227H
109 3 142987786 C T synonymous P547P 472 3 143371174 C A synonymous L226L
110 3 142987787 G A nonsynonymous P547L 473 3 143371176 G A synonymous L226L
111 3 142987790 G C nonsynonymous P546R 474 3 143371176 G C nonsynonymous L226V
112 3 142987793 C T nonsynonymous G545D 475 3 143371182 G A nonsynonymous H224Y
113 3 142987796 G A nonsynonymous S544F 476 3 143371188 T C nonsynonymous I222V
1 2 3 4 5 6 7 8 9 10 11 12 13 14
114 3 142987797 A - frameshift deletion S544Lfs*4 477 3 143371189 G A synonymous A221A
115 3 142987797 A G nonsynonymous S544P 478 3 143371194 G A synonymous L220L
116 3 142987801 G A synonymous T542T 479 3 143371196 A G nonsynonymous V219A
117 3 142987801 G C synonymous T542T 480 3 143371198 T C synonymous T218T
118 3 142987802 G A nonsynonymous T542I 481 3 143371199 G A nonsynonymous T218I
119 3 142987803 T A nonsynonymous T542S 482 3 143371201 C T synonymous V217V
120 3 142987807 A T synonymous I540I 483 3 143371202 A G nonsynonymous V217A
121 3 142987809 T C nonsynonymous I540V 484 3 143412035 T C synonymous P216P
122 3 142987812 G C nonsynonymous P539A 485 3 143412036 G A nonsynonymous P216L
123 3 142987819 A G synonymous Y536Y 486 3 143412037 G T nonsynonymous P216T
124 3 142987820 - A frameshift insertion Y536Lfs*18 487 3 143412040 C G nonsynonymous D215H
125 3 142987822 C T synonymous K535K 488 3 143412041 T C synonymous T214T
126 3 143082326 T C nonsynonymous K535R 489 3 143412043 T C nonsynonymous T214A
127 3 143082328 G A synonymous H534H 490 3 143412051 A C nonsynonymous M211R
128 3 143082329 T G nonsynonymous H534P 491 3 143412052 T A nonsynonymous M211L
129 3 143082330 G A nonsynonymous H534Y 492 3 143412054 A G nonsynonymous L210P
130 3 143082331 G A synonymous D533D 493 3 143412061 C A nonsynonymous G208C
131 3 143082336 A C nonsynonymous F532V 494 3 143412066 A T nonsynonymous F206Y
132 3 143082337 G - frameshift deletion F532Lfs*5 495 3 143412067 A G nonsynonymous F206L
133 3 143082337 G C nonsynonymous S531R 496 3 143412068 T C synonymous L205L
134 3 143082337 G T nonsynonymous S531R 497 3 143412078 G A nonsynonymous T202I
135 3 143082338 C T nonsynonymous S531N 498 3 143412085 - A frameshift insertion H200Sfs*3
136 3 143082340 A G synonymous Y530Y 499 3 143412090 T G nonsynonymous D198A
137 3 143082343 C T stopgain W529X 500 3 143412103 G T nonsynonymous L194M
138 3 143082344 C G nonsynonymous W529S 501 3 143412105 T - frameshift deletion Q193Rfs*1
139 3 143082347 A T nonsynonymous M528K 502 3 143412106 G A stopgain Q193X
140 3 143082351 T G synonymous R527R 503 3 143412107 G T synonymous G192G
141 3 143082352 G C nonsynonymous F526L 504 3 143412111 G A nonsynonymous A191V
142 3 143082355 G A synonymous L525L 505 3 143412113 A G synonymous H190H
143 3 143082358 C G synonymous R524R 506 3 143412114 T G nonsynonymous H190P
144 3 143082359 C T nonsynonymous R524Q 507 3 143412118 T A nonsynonymous I189L
145 3 143082360 G A nonsynonymous R524W 508 3 143412120 A G nonsynonymous M188T
146 3 143082360 G C nonsynonymous R524G 509 3 143412121 T C nonsynonymous M188V
147 3 143082364 A G synonymous S522S 510 3 143412124 C A nonsynonymous A187S
148 3 143082365 CT - frameshift deletion S522Cfs*8 511 3 143412124 C T nonsynonymous A187T
149 3 143082367 C G nonsynonymous E521D 512 3 143412125 C T synonymous K186K
150 3 143082371 G T nonsynonymous A520E 513 3 143412129 A C nonsynonymous V185G
151 3 143082373 T G nonsynonymous K519N 514 3 143412134 A G synonymous G183G
152 3 143082374 T C nonsynonymous K519R 515 3 143412137 A G synonymous Y182Y
153 3 143082376 C T synonymous T518T 516 3 143412138 T A nonsynonymous Y182F
154 3 143082377 G A nonsynonymous T518M 517 3 143412138 T C nonsynonymous Y182C
155 3 143082379 C T nonsynonymous M517I 518 3 143412139 A G nonsynonymous Y182H
156 3 143082385 T C synonymous K515K 519 3 143412141 A G nonsynonymous M181T
157 3 143082387 T A stopgain K515X 520 3 143412142 T C nonsynonymous M181V
1 2 3 4 5 6 7 8 9 10 11 12 13 14
158 3 143082389 T C nonsynonymous D514G 521 3 143412143 A - frameshift deletion M181Cfs*4
159 3 143082392 A G nonsynonymous L513S 522 3 143412144 A T nonsynonymous I180N
160 3 143082395 T G nonsynonymous N512T 523 3 143412148 A C nonsynonymous L179V
161 3 143082401 G A nonsynonymous A510V 524 3 143412149 C A synonymous G178G
162 3 143082402 C T nonsynonymous A510T 525 3 143513843 C T nonsynonymous G178E
163 3 143082404 T C nonsynonymous E509G 526 3 143513848 G C synonymous V176V
164 3 143100902 C T synonymous Q508Q 527 3 143513849 A T nonsynonymous V176D
165 3 143100903 T C nonsynonymous Q508R 528 3 143513850 C T nonsynonymous V176I
166 3 143100908 T G nonsynonymous Q506H 529 3 143513851 G A synonymous I175I
167 3 143100914 G A synonymous S504S 530 3 143513855 C A nonsynonymous C174F
168 3 143100914 G C synonymous S504S 531 3 143513857 G C synonymous S173S
169 3 143100917 G C synonymous P503P 532 3 143513866 A G synonymous T170T
170 3 143100919 G T nonsynonymous P503T 533 3 143513868 T G nonsynonymous T170P
171 3 143100920 G T nonsynonymous D502E 534 3 143513872 C G nonsynonymous L168F
172 3 143100922 C T nonsynonymous D502N 535 3 143513874 A G synonymous L168L
173 3 143100923 C G nonsynonymous E501D 536 3 143513875 G A synonymous F167F
174 3 143100923 C T synonymous E501E 537 3 143513878 G A synonymous A166A
175 3 143100926 C T synonymous K500K 538 3 143513881 A G synonymous Y165Y
176 3 143100927 T G nonsynonymous K500T 539 3 143513882 T G nonsynonymous Y165S
177 3 143100930 A G nonsynonymous L499P 540 3 143513884 C A synonymous T164T
178 3 143100932 A T nonsynonymous N498K 541 3 143513884 C T synonymous T164T
179 3 143100933 T C nonsynonymous N498S 542 3 143513885 G A nonsynonymous T164M
180 3 143100935 T G nonsynonymous E497D 543 3 143513886 T A nonsynonymous T164S
181 3 143100939 T C nonsynonymous D496G 544 3 143513886 - TA stopgain T164fs*0
182 3 143100940 C T nonsynonymous D496N 545 3 143513889 A G synonymous L163L
183 3 143100942 A G nonsynonymous L495P 546 3 143513890 A G synonymous I162I
184 3 143100944 G A synonymous D494D 547 3 143513895 A T nonsynonymous S161T
185 3 143100946 C T nonsynonymous D494N 548 3 143513896 T A synonymous G160G
186 3 143100947 C T synonymous V493V 549 3 143513897 C A nonsynonymous G160V
187 3 143100948 A G nonsynonymous V493A 550 3 143513897 C G nonsynonymous G160A
188 3 143100949 C T nonsynonymous V493M 551 3 143513897 C T nonsynonymous G160E
189 3 143100950 G A synonymous G492G 552 3 143513898 C T nonsynonymous G160R
190 3 143100952 C T nonsynonymous G492S 553 3 143513902 G A synonymous N158N
191 3 143100956 T C synonymous R490R 554 3 143513907 G A stopgain Q157X
192 3 143185879 C T nonsynonymous R490K 555 3 143513908 A G synonymous F156F
193 3 143185882 A G nonsynonymous I489T 556 3 143513914 G A synonymous H154H
194 3 143185885 T G nonsynonymous Q488P 557 3 143513918 C T nonsynonymous R153K
195 3 143185886 G A stopgain Q488X 558 3 143513919 T C nonsynonymous R153G
196 3 143185894 G A nonsynonymous T485I 559 3 143515670 T G nonsynonymous K152Q
197 3 143185894 G C nonsynonymous T485S 560 3 143515674 T A synonymous L150L
198 3 143185902 G A synonymous P482P 561 3 143515678 C T nonsynonymous S149N
199 3 143185903 G T nonsynonymous P482H 562 3 143515683 T C synonymous G147G
200 3 143185904 G A nonsynonymous P482S 563 3 143515687 G A nonsynonymous A146V
201 3 143185904 G T nonsynonymous P482T 564 3 143515688 C A nonsynonymous A146S
202 3 143185906 G A nonsynonymous T481I 565 3 143515689 A G synonymous H145H
203 3 143185906 G T nonsynonymous T481N 566 3 143515692 A G synonymous F144F
204 3 143185907 T G nonsynonymous T481P 567 3 143515697 T C nonsynonymous I143V
205 3 143185910 T C nonsynonymous T480A 568 3 143515705 G A nonsynonymous P140L
206 3 143185911 T C synonymous G479G 569 3 143515706 G A nonsynonymous P140S
207 3 143185912 C T nonsynonymous G479E 570 3 143515706 G T nonsynonymous P140T
1 2 3 4 5 6 7 8 9 10 11 12 13 14
208 3 143185913 C T nonsynonymous G479R 571 3 143515709 G A synonymous L139L
209 3 143185915 C T nonsynonymous G478E 572 3 143515715 C T nonsynonymous V137I
210 3 143185920 A G synonymous F476F 573 3 143515717 T C nonsynonymous N136S
211 3 143185923 T A synonymous V475V 574 3 143515718 T G nonsynonymous N136H
212 3 143185923 T G synonymous V475V 575 3 143515719 GAA - nonframeshift deletion F135del
213 3 143185926 C T stopgain W474X 576 3 143515719 G A synonymous F135F
214 3 143185929 G A synonymous V473V 577 3 143515724 A C nonsynonymous F134V
215 3 143185938 G A synonymous F470F 578 3 143515731 T A synonymous P131P
216 3 143185943 C T nonsynonymous V469M 579 3 143550860 CCTTTT - frameshift deletion E125Dfs*3
217 3 143185944 G A synonymous L468L 580 3 143550861 CTTTT - frameshift deletion E125Dfs*3
218 3 143185947 G C synonymous L467L 581 3 143550864 T C synonymous E125E
219 3 143185949 G A nonsynonymous L467F 582 3 143550870 T A synonymous I123I
220 3 143185951 A G nonsynonymous L466P 583 3 143550871 A G nonsynonymous I123T
221 3 143185953 C T synonymous T465T 584 3 143550872 T C nonsynonymous I123V
222 3 143185954 G A nonsynonymous T465M 585 3 143550873 A G synonymous A122A
223 3 143185955 T A nonsynonymous T465S 586 3 143550874 G A nonsynonymous A122V
224 3 143185955 T C nonsynonymous T465A 587 3 143550875 C A nonsynonymous A122S
225 3 143185956 A G synonymous T464T 588 3 143550884 G T nonsynonymous Q119K
226 3 143185958 T C nonsynonymous T464A 589 3 143550886 T C nonsynonymous H118R
227 3 143185964 A G nonsynonymous F462L 590 3 143550890 G T nonsynonymous P117T
228 3 143185966 A G nonsynonymous M461T 591 3 143550892 T C nonsynonymous N116S
229 3 143185968 C A nonsynonymous M460I 592 3 143550896 TGT - nonframeshift deletion N114del
230 3 143185968 C T nonsynonymous M460I 593 3 143550900 G A synonymous H113H
231 3 143185970 T C nonsynonymous M460V 594 3 143550903 C A nonsynonymous Q112H
232 3 143185974 T G nonsynonymous K458N 595 3 143550911 T C nonsynonymous I110V
233 3 143185975 T C nonsynonymous K458R 596 3 143550916 C - frameshift deletion R108Kfs*2
234 3 143185979 G T nonsynonymous P457T 597 3 143550916 C T nonsynonymous R108K
235 3 143185980 C G nonsynonymous Q456H 598 3 143550917 T A stopgain R108X
236 3 143185980 C T synonymous Q456Q 599 3 143550920 T C nonsynonymous K107E
237 3 143185984 G A nonsynonymous S455F 600 3 143550921 G A synonymous Y106Y
238 3 143185993 T C nonsynonymous N452S 601 3 143550935 A G nonsynonymous Y102H
239 3 143185995 C G synonymous R451R 602 3 143550941 G C nonsynonymous Q100E
240 3 143185996 C T nonsynonymous R451Q 603 3 143550945 A G synonymous T98T
241 3 143185997 G A nonsynonymous R451W 604 3 143550946 G C nonsynonymous T98S
242 3 143185998 A C nonsynonymous I450M 605 3 143550954 A - frameshift deletion N96Ifs*14
243 3 143186003 C T nonsynonymous A449T 606 3 143550956 C T nonsynonymous V95I
244 3 143186006 A G synonymous L448L 607 3 143550957 C G synonymous L94L
245 3 143186013 T C synonymous A445A 608 3 143550960 C G synonymous L93L
246 3 143186015 C T nonsynonymous A445T 609 3 143550965 T C nonsynonymous T92A
247 3 143186016 G A synonymous I444I 610 3 143550965 T G nonsynonymous T92P
248 3 143186016 G T synonymous I444I 611 3 143550967 G A nonsynonymous S91L
249 3 143186017 A G nonsynonymous I444T 612 3 143550971 G T nonsynonymous P90T
250 3 143186019 C A synonymous A443A 613 3 143550974 T C nonsynonymous S89G
251 3 143186019 C T synonymous A443A 614 3 143550979 G A nonsynonymous T87I
252 3 143186020 G A nonsynonymous A443V 615 3 143550979 G T nonsynonymous T87N
1 2 3 4 5 6 7 8 9 10 11 12 13 14
253 3 143186021 C T nonsynonymous A443T 616 3 143550982 A C nonsynonymous L86R
254 3 143186022 T G synonymous G442G 617 3 143550982 A G nonsynonymous L86P
255 3 143186026 C T nonsynonymous R441Q 618 3 143550983 G A synonymous L86L
256 3 143186027 G A stopgain R441X 619 3 143550983 G C nonsynonymous L86V
257 3 143186029 A G nonsynonymous L440S 620 3 143550990 A T stopgain C83X
258 3 143212495 C T nonsynonymous G439S 621 3 143550992 A C nonsynonymous C83G
259 3 143212498 A G nonsynonymous S438P 622 3 143550996 A G synonymous Y81Y
260 3 143212506 A G nonsynonymous M435T 623 3 143550996 A T stopgain Y81X
261 3 143212506 A T nonsynonymous M435K 624 3 143551000 A C nonsynonymous V80G
262 3 143212510 T A nonsynonymous M434L 625 3 143551000 A G nonsynonymous V80A
263 3 143212511 G A synonymous H433H 626 3 143551003 G C nonsynonymous T79S
264 3 143212511 G T nonsynonymous H433Q 627 3 143551004 T A nonsynonymous T79S
265 3 143212515 T C nonsynonymous Q432R 628 3 143551004 T C nonsynonymous T79A
266 3 143212517 A G synonymous F431F 629 3 143551009 C T nonsynonymous S77N
267 3 143212519 A T nonsynonymous F431I 630 3 143551011 T G nonsynonymous E76D
268 3 143212521 T C nonsynonymous N430S 631 3 143551021 G A nonsynonymous T73I
269 3 143212522 T C nonsynonymous N430D 632 3 143551021 G C nonsynonymous T73S
270 3 143212530 A G nonsynonymous I427T 633 3 143551022 T C nonsynonymous T73A
271 3 143212531 T C nonsynonymous I427V 634 3 143551023 T G synonymous P72P
272 3 143212542 C T nonsynonymous R423Q 635 3 143551032 A G synonymous A69A
273 3 143212543 G A stopgain R423X 636 3 143551035 A G synonymous Y68Y
274 3 143212546 C T nonsynonymous G422S 637 3 143551037 A T nonsynonymous Y68N
275 3 143212559 G A synonymous F417F 638 3 143551038 T C synonymous R67R
276 3 143212564 A T nonsynonymous S416T 639 3 143551039 C A nonsynonymous R67L
277 3 143212567 G A nonsynonymous L415F 640 3 143551039 C G nonsynonymous R67P
278 3 143212568 G A synonymous P414P 641 3 143551039 C T nonsynonymous R67Q
279 3 143212570 G T nonsynonymous P414T 642 3 143551040 G A stopgain R67X
280 3 143212574 T C nonsynonymous I412M 643 3 143551044 A T synonymous I65I
281 3 143212577 G A synonymous N411N 644 3 143551048 A G nonsynonymous L64P
282 3 143212577 G T nonsynonymous N411K 645 3 143551049 G A synonymous L64L
283 3 143212578 T C nonsynonymous N411S 646 3 143551051 C A nonsynonymous G63V
284 3 143212582 A T nonsynonymous C410S 647 3 143551053 C G nonsynonymous M62I
285 3 143212584 G A nonsynonymous A409V 648 3 143551053 C T nonsynonymous M62I
286 3 143212584 G C nonsynonymous A409G 649 3 143551054 A G nonsynonymous M62T
287 3 143212584 G T nonsynonymous A409D 650 3 143551055 T C nonsynonymous M62V
288 3 143212585 C G nonsynonymous A409P 651 3 143551057 A G nonsynonymous I61T
289 3 143212586 T C synonymous R408R 652 3 143551057 A T nonsynonymous I61K
290 3 143212594 C T nonsynonymous V406I 653 3 143551059 A T synonymous L60L
291 3 143212597 A G nonsynonymous F405L 654 3 143551061 GGCCT - nonframeshift deletion G59_L60de-linsV
292 3 143212599 A G nonsynonymous I404T 655 3 143551063 C T nonsynonymous G59D
293 3 143212599 A T nonsynonymous I404N 656 3 143566990 C T nonsynonymous G59S
294 3 143212606 G A synonymous L402L 657 3 143566991 A G synonymous Y58Y
295 3 143214180 G A synonymous A400A 658 3 143566994 C A synonymous V57V
296 3 143214181 G C nonsynonymous A400G 659 3 143567000 T C synonymous A55A
297 3 143214181 G T nonsynonymous A400D 660 3 143567001 G A nonsynonymous A55V
298 3 143214182 C T nonsynonymous A400T 661 3 143567002 C T nonsynonymous A55T
299 3 143214184 C T nonsynonymous G399E 662 3 143567004 C T nonsynonymous G54E
300 3 143214188 G C nonsynonymous L398V 663 3 143567006 T A synonymous G53G
301 3 143214189 T C nonsynonymous I397M 664 3 143567011 T A nonsynonymous T52S
302 3 143214195 A C synonymous L395L 665 3 143567014 C G nonsynonymous E51Q
1 2 3 4 5 6 7 8 9 10 11 12 13 14
303 3 143214197 G C nonsynonymous L395V 666 3 143567017 G C nonsynonymous H50D
304 3 143214198 A G synonymous A394A 667 3 143567018 C T synonymous L49L
305 3 143214199 G A nonsynonymous A394V 668 3 143567025 C A nonsynonymous R47L
306 3 143214209 T C nonsynonymous I391V 669 3 143567025 C T nonsynonymous R47H
307 3 143214212 G T nonsynonymous H390N 670 3 143567026 G A nonsynonymous R47C
308 3 143214213 A T nonsynonymous N389K 671 3 143567031 C A nonsynonymous R45L
309 3 143214222 C T synonymous T386T 672 3 143567032 G T synonymous R45R
310 3 143214223 G A nonsynonymous T386M 673 3 143567033 A G synonymous H44H
311 3 143214226 A T nonsynonymous F385Y 674 3 143567036 A T nonsynonymous N43K
312 3 143214227 A G nonsynonymous F385L 675 3 143567038 T C nonsynonymous N43D
313 3 143214231 T C synonymous A383A 676 3 143567043 A G nonsynonymous F41S
314 3 143214237 G A synonymous G381G 677 3 143567047 A G synonymous L40L
315 3 143214242 T C nonsynonymous M380V 678 3 143567048 C T stopgain W39X
316 3 143214244 T G nonsynonymous Y379S 679 3 143567049 C T stopgain W39X
317 3 143214248 A G nonsynonymous C378R 680 3 143567051 G A synonymous I38I
318 3 143214249 G A synonymous F377F 681 3 143567052 A G nonsynonymous I38T
319 3 143214251 A G nonsynonymous F377L 682 3 143567053 T C nonsynonymous I38V
320 3 143214257 C G nonsynonymous V375L 683 3 143567055 G T nonsynonymous T37K
321 3 143214257 C T nonsynonymous V375I 684 3 143567059 A G synonymous L36L
322 3 143214258 G A synonymous N374N 685 3 143567061 A G nonsynonymous I35T
323 3 143214259 T C nonsynonymous N374S 686 3 143567067 A C nonsynonymous L33R
324 3 143214262 T C nonsynonymous E373G 687 3 143567073 A T nonsynonymous L31H
325 3 143214264 C T synonymous A372A 688 3 143567074 G A nonsynonymous L31F
326 3 143214265 G A nonsynonymous A372V 689 3 143567075 - A frameshift insertion L30Ffs*12
327 3 143214266 C A nonsynonymous A372S 690 3 143567080 A C nonsynonymous F29V
328 3 143214276 C T nonsynonymous M368I 691 3 143567081 A G synonymous N28N
329 3 143214286 A G nonsynonymous F365S 692 3 143567087 G A synonymous V26V
330 3 143271204 C T synonymous Q363Q 693 3 143567095 G A synonymous L24L
331 3 143271205 T C nonsynonymous Q363R 694 3 143567096 C G nonsynonymous E23D
332 3 143271206 G T nonsynonymous Q363K 695 3 143567100 A C nonsynonymous V22G
333 3 143271207 T C synonymous K362K 696 3 143567100 A T nonsynonymous V22E
334 3 143271211 G C nonsynonymous T361S 697 3 143567103 G A nonsynonymous A21V
335 3 143271218 T C nonsynonymous I359V 698 3 143567110 G C nonsynonymous Q19E
336 3 143271220 T G nonsynonymous K358T 699 3 143567111 A T nonsynonymous H18Q
337 3 143271222 G A synonymous S357S 700 3 143567112 T C nonsynonymous H18R
338 3 143271227 C G nonsynonymous D356H 701 3 143567125 A G nonsynonymous Y14H
339 3 143271228 C T synonymous S355S 702 3 143567126 C G nonsynonymous E13D
340 3 143271229 G A nonsynonymous S355L 703 3 143567126 C T synonymous E13E
341 3 143271238 T C nonsynonymous N352S 704 3 143567129 A C nonsynonymous D12E
342 3 143271240 G A synonymous N351N 705 3 143567129 A G synonymous D12D
343 3 143271240 G C nonsynonymous N351K 706 3 143567131 C T nonsynonymous D12N
344 3 143271241 T C nonsynonymous N351S 707 3 143567132 C T synonymous K11K
345 3 143271242 T C nonsynonymous N351D 708 3 143567133 T C nonsynonymous K11R
346 3 143271243 G C stopgain Y350X 709 3 143567133 T G nonsynonymous K11T
347 3 143271249 A G synonymous Y348Y 710 3 143567137 C G nonsynonymous E10Q
348 3 143271250 T C nonsynonymous Y348C 711 3 143567138 T C synonymous S9S
349 3 143271254 G A nonsynonymous H347Y 712 3 143567140 A C nonsynonymous S9A
350 3 143271257 C T nonsynonymous A346T 713 3 143567141 C T nonsynonymous M8I
351 3 143271263 T A nonsynonymous T344S 714 3 143567146 C A nonsynonymous V7F
352 3 143271268 C T nonsynonymous G342E 715 3 143567146 C T nonsynonymous V7I
1 2 3 4 5 6 7 8 9 10 11 12 13 14
353 3 143271281 C G nonsynonymous V338L 716 3 143567148 C G nonsynonymous R6T
354 3 143271283 G A nonsynonymous A337V 717 3 143567148 C T nonsynonymous R6K
355 3 143271284 C A nonsynonymous A337S 718 3 143567150 T C synonymous S5S
356 3 143271286 A T nonsynonymous V336D 719 3 143567151 G T stopgain S5X
357 3 143271290 T A nonsynonymous I335L 720 3 143567154 T G nonsynonymous Q4P
358 3 143271292 C T nonsynonymous G334E 721 3 143567156 TC - frameshift deletion R3Tfs*9
359 3 143292930 C T nonsynonymous G334R 722 3 143567157 C T nonsynonymous R3K
360 3 143292931 T C synonymous T333T 723 3 143567160 T G nonsynonymous E2A
361 3 143292932 G A nonsynonymous T333I 724 3 143567163 A C startloss E2 M8del
362 3 143292938 C T nonsynonymous G331D 725 3 143567164 T A startloss E2 M8del
363 3 143292939 C nonsynonymous T G331S
Table 2. - SNPs associated with cancer
Chr Position Ref Alt dbSNP COSMIC_ID Cancer type Exonic Function AAChange
1 2 3 4 5 6 7 8 9
3 142985638 G A rs767114012 COSM5987135 salivary gland nonsynonymous T615M
3 142985708 G A rs752770927 C0SM1039503 endometrium stopgain Q592X
3 142985753 C T rs757449602 C0SM3125514 upper aerodi-gestive tract nonsynonymous D577N
3 142987786 C T rs61750363 C0SM1039505 endometrium synonymous P547P
3 143082359 C T rs769786135 C0SM5664679 lung nonsynonymous R524Q
3 143082360 G A rs574582502 C0SM1226613 large intestine nonsynonymous R524W
3 143082373 T G rs771266539 C0SM3125518 stomach nonsynonymous K519N
3 143082376 C T rs141051651 C0SM3427182 large intestine synonymous T518T
3 143082377 G A rs759634686 C0SM728924 lung; large intestine nonsynonymous T518M
3 143100923 C T rs747034373 C0SM3915071 skin synonymous E501E
3 143100949 C T rs775249012 C0SM3783668 bone; oesophagus; prostate; large intestine nonsynony-mous V493M
3 143100950 G A rs201448381 C0SM383360 lung; endometrium synonymous G492G
3 143185912 C T rs143224544 C0SM107028 skin nonsynonymous G479E
3 143185920 A G rs61734421 C0SM4114204 stomach synonymous F476F
3 143185943 C T rs768229420 C0SM4584016 bone nonsynonymous V469M
3 143185954 G A rs771359670 C0SM1419701 large intestine nonsynonymous T465M
3 143185968 C T rs761372851 C0SM3588352 skin nonsynonymous M460I
1 2 3 4 5 6 7 8 9
3 143185970 T C rs61734409 C0SM3846440 breast nonsynonymous M460V
3 143185984 G A rs759376193 C0SM3846441 breast; NS nonsynonymous S455F
3 143185997 G A rs752878648 C0SM205616 skin nonsynonymous R451W
3 143186015 C T rs761337323 C0SM5549901 prostate nonsynonymous A445T
3 143186016 G A rs141105678 C0SM3588354 oesophagus; skin synonymous I444I
3 143186019 C T rs144930120 C0SM5604940 skin synonymous A443A
3 143212542 C T rs368254745 C0SM3125528 large intestine nonsynonymous R423Q
3 143212543 G A rs121912597 C0SM5455144 large intestine stopgain R423X
3 143214209 T C rs138653730 C0SM4114206 stomach nonsynonymous I391V
3 143214222 C T rs140335350 C0SM5007475 large intestine synonymous T386T
3 143214258 G A rs137994789 C0SM1266084 stomach synonymous N374N
3 143214264 C T rs533183607 C0SM1039507 liver; endometrium synonymous A372A
3 143271229 G A rs552019939 C0SM1039509 stomach; endometrium nonsynonymous S355L
3 143292940 G T rs140574815 C0SM4319719 bone synonymous A330A
3 143293003 C T rs144088456 C0SM4727884 bone; large intestine synonymous P309P
3 143293004 G A rs775325802 C0SM3846442 breast nonsynonymous P309L
3 143293012 A G rs6763202 C0SM4406945 haematopoietic and lymphoid tissue; liver synonymous C306C
3 143297448 C T rs140901762 C0SM1039511 endometrium synonymous A291A
3 143297516 C T rs143468139 C0SM3001742 small intestine nonsynonymous A269T
3 143297517 G A rs759374253 C0SM5026058 breast synonymous A268A
3 143371182 G A rs778413733 C0SM4901315 skin nonsynonymous H224Y
3 143371201 C T rs1242069 C0SM3759808 large intestine synonymous V217V
3 143513851 G A rs377682237 C0SM1536649 skin; lung synonymous I175I
3 143513878 G A rs752509231 C0SM4497507 skin synonymous A166A
3 143513885 G A rs201948779 C0SM4781526 pancreas nonsynonymous T164M
3 143513907 G A rs866080325 C0SM3588362 skin stopgain Q157X
3 143550892 T C rs762785258 C0SM4998907 pancreas nonsynonymous N116S
3 143550916 C T rs767428360 C0SM6096454 !ung nonsynonymous R108K
1 2 3 4 5 6 7 8 9
3 143551032 A G rs112237207 COSM728916 lung synonymous A69A
3 143551039 C T rs372558008 C0SM1039515 endometrium nonsynony-mous R67Q
3 143567075 - A rs765712953 C0SM1180943 large intestine frameshift insertion L30Ffs*12
3 143567080 A C rs534139654 C0SM1419714 large intestine nonsynony-mous F29V
Table 3. - GWAS Catalog SLC9A9 associations with disease
Variant and risk allele P-val-ue P-value annotation RAF OR Beta CI Trait(s)
1 2 3 4 5 6 7 8
rs7632299-A 4 x 10-6 0.17 - 0.45 unit increase [NR] non-alcoholic fatty liver disease, cirrhosis of liver
rs7645841-? 5 x 10-6 NR - - - QT interval, Trypanosoma cruzi seropositivity
response to platinum based
rs201023017-? 6 x 10-7 NR - - - chemotherapy, ovarian carcinoma, cytotoxicity measurement, response to paclitaxel
rs185347221-A 4 x 10-6 0.0011 - 1.7791 unit increase [1.022.54] BMI-adjusted hip circumference
(G0:0015238
rs10935496-A 3 x 10-8 |MF|03|drug transmembrane NR 5.527629 Z-score NR gut microbiome measurement
transporter activity) decrease
forced expiratory volume, al-
rs35312258-G 4 x 10-6 0.17 - — - lergen exposure measurement, asthma
rs1875463-? 2 x 10-6 NR 1.111605 - - rheumatoid arthritis
rs1135438-? 9 x 10-6 NR - - - radius bone mineral density
rs1868175-A 7 x 10-17 0.748 - 0.22 unit increase [0.170.27] HIV-1 infection, viral load
rs12637224-
G, rs16853354-
G, rs1501626-
G, rs7641708-
G, rs2197063-A, rs17636071- 1 x 10-7 0.009 - - - acute myeloid leukemia
T, rs7617034-
A, rs7639109-
C, rs16853335-
A
1 2 3 4 5 6 7 8
rs35312258-G 4 x 10-6 0.17 - - - forced expiratory volume, allergen exposure measurement, asthma
rs1875463-? 2 x 10-6 NR 1.111605 - - rheumatoid arthritis
rs1135438-? 9 x 10-6 NR - - - radius bone mineral density
rs1868175-A 7 x 10-17 0.748 - 0.22 unit increase [0.170.27] HIV-1 infection, viral load
rs12637224-G, rs16853354-G, rs1501626-G, rs7641708-G, rs2197063-A, rs17636071-T, rs7617034-A, rs7639109-C, rs16853335-A 1 x 10-7 0.009 - - - acute myeloid leukemia
rs1372288-C, rs294470-G 7 x 10-9 0.201 - - - acute myeloid leukemia
rs9810857-T 6 x 10-6 0.49 1.41 - [NR] attention deficit hyperactivity disorder
rs294468-? 6 x 10-9 NR - - - mean corpuscular hemoglobin
rs2800-G 3 x 10-6 (ALT) 0.34 - 0.61 unit increase [NR] serum alanine aminotransfer-ase measurement, non-alcoholic fatty liver disease
rs1371924-? 4 x 10-6 (RWLTA) NR - - - blood pressure
rs2166775-G 3 x 10-6 (EA) NR - 0.99 unit increase [0.541.44] response to candesartan, hypertension
rs17636071-G 2 x 10-6 (MMSE) 0.09 - 4.74 unit decrease [NR] response to cholinesterase inhibitor, Alzheimer's disease
rs1404568-G 2 x 10-6 0.18 - - - forced expiratory volume, allergen exposure measurement, asthma
rs4839603-C 4 x 10-6 (additive model) NR - 0.03503 unit decrease - response to opioid, analgesia requirement measurement
rs115134572-? 6 x 10-7 - - 0.4727 unit decrease [NR] sporadic amyotrophic lateral sclerosis, survival time
rs17635531-A 7 x 10-7 (sleep duration) NR - 0.403 unit decrease [0.240.56] sleep duration
rs4839604-A 4 x 10-13 (Tetrasialylat-ed) 0.23 - 0.22375393 (zscore) increase [0.160.28] N-glycan measurement
1 2 3 4 5 6 7 8
rsl372288-G 3 x 10-8 (Tetrasialylated, men) 0.25 - 0.24889249 (zscore) increase [0.160.34] N-glycan measurement
Table 4. - A summary information of two disease SNPs related to ADHD or ASD
rs1248614031 rs121912597
Organism Homo sapiens Homo sapiens
Position chr3:143493743 (GRCh38.p12) chr3:143493701 (GRCh38.p12)
Alleles C>G G>A
Variation Type SNV Single Nucleotide Variation SNV Single Nucleotide Variation
Frequency G=0.00000 (1/251382, Gno-mAD exome) A=0.00005 (12/251342, GnomAD_exome) A=0.00002 (3/121390, ExAC) A=0.0000 (1/78696, PAGE_STUDY) (- 2 less) A=0.0000 (1/31388, GnomAD) A=0.000 (1/5008, 1000G)
Gene: Consequence SLC9A9 : Missense Variant SLC9A9 : Stop Gained
Code GCC to ACC CGA to TGA
Amino acid change A409P R423X
Protein domain cation/H+ exchanger domain cation/H+ exchanger domain
Protein interaction Yes Yes
Topology not in transmembrane helix not in transmembrane helix
Active site No No
Stability No No
Expression No No
References:
1. Zhang-James Y., Vaudel M., Mjaavatten O., Berven F. S., HaavikJ., Faraone S. V. Effect of disease-associated SLC9A9 mutations on protein-protein interaction networks: implications for molecular mechanisms for ADHD and autism. Atten Defic Hyperact Disord. 2019. Mar;11 (1): 91-105.
2. De Rubeis S., Buxbaum J. D. Genetics and genomics of autism spectrum disorder: embracing complexity. Hum Mol Genet. 2015. Oct. 15; 24 (R1): R24-31.
3. National Institute ofMental Health (2019). Attention-Deficit / Hyperactivity Disorder. RetrievedJanuary 1, 2020. From: URL: https://www.nimh.nih.gov/health/topics/attention-deficit-hyperactivity-disorder-adhd/index.shtml.
4. Morrow E. M., Yoo S. Y., Flavell S. W., Kim T. K., Lin Y., Hill R. S., Mukaddes N. M., Balkhy S., Gascon G., Hashmi A., Al-Saad S., Ware J., Joseph R. M., Greenblatt R., Gleason D., Ertelt J. A., Apse K. A., Bodell A., Partlow J. N., Barry B., Yao H., Markianos K., Ferland R.J., Greenberg M. E., Walsh C. A. Identifying autism loci and genes by tracing recent shared ancestry. Science. 2008. Jul. 11; 321(5886): 218-23.
5. Patak J., Zhang-James Y., Faraone S. V. Endosomal system genetics and autism spectrum disorders: A literature review. Neurosci Biobehav Rev. 2016. Jun; 65: 95-112.
6. Zhang-James Y., DasBanerjee T., Sagvolden T., Middleton F. A., Faraone S. V. SLC9A9 mutations, gene expression, and protein-protein interactions in rat models of attention-deficit/hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet. 2011. Dec; 156B(7): 835-43.
7. Zhang-James Y., Middleton F. A., Sagvolden T., Faraone S. V. Differential expression of SLC9A9 and interacting molecules in the hippocampus of rat models for attention deficit/hyperactivity disorder. Dev Neurosci. 2012; 34(2-3): 218-27.
8. Cingolani H. E., Ennis I. L. Sodium-Hydrogen Exchanger, Cardiac Overload, and Myocardial Hypertrophy. Circulation. 2007. Mar; 115: 1090-1100.
9. Kondapalli K. C., Prasad H. and Rao R. An inside job: how endosomal Na+/H+ exchangers link to autism and neurological disease. Front. Cell. Neurosci. 8: 2014; 172. Doi: 10.3389/fncel.2014.00172.
