Single Nucleotide Polymorphism Database Research Articles

Novel Germline Mutations of BRCA1 and BRCA2 in Korean Familial Breast Cancer Patients.

Breast cancer is the second most common cancer in Korean women. Germline mutations in the BRCA1 and BRCA2 genes cause hereditary breast cancer and are detected in 15–20% of hereditary breast cancer. We investigated the BRCA1 and BRCA2 mutations in 114 familial breast cancer patients using next-generation sequencing. We confirmed 20 different mutations of BRCA1 and BRCA2 in 25 subjects (21.9%). Two such mutations in eight patients were novel (not reported in any variant database or previous study). Six mutations have been reported as disease-causing mutations in public databases. Seven mutations were found only in a single nucleotide polymorphism database and one mutation has been reported in Korea. The BRCA1/2 mutation frequency was similar to that of other studies on familial breast cancer patients in the Korean population. Further studies should examine more cases and mutations of whole exons.

An effective biomedical data migration tool from resource description framework to JSON.

Resource Description Framework (RDF) is widely used for representing biomedical data in practical applications. With the increases of RDF-based applications, there is an emerging requirement of novel architectures to provide effective supports for the future RDF data explosion. Inspired by the success of the new designs in National Center for Biotechnology Information dbSNP (The Single Nucleotide Polymorphism Database) for managing the increasing data volumes using JSON (JavaScript Object Notation), in this paper we present an effective mapping tool that allows data migrations from RDF to JSON for supporting future massive data explosions and releases. We firstly introduce a set of mapping rules, which transform an RDF format into the JSON format, and then present the corresponding transformation algorithm. On this basis, we develop an effective and user-friendly tool called RDF2JSON, which enables automating the process of RDF data extractions and the corresponding JSON data generations.

Pan-cancer repository of validated natural and cryptic mRNA splicing mutations

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 351,423 of these validated mutations, the majority of which (69.1%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 117,951 unique mutations which weaken or abolish natural splice sites, and 244,415 mutations which strengthen cryptic splice sites (10,943 affect both simultaneously). 27,803 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon “Validated Splicing Mutations” either separately or in aggregate alongside other Beacons through the public Beacon Network (http://www.beacon-network.org/#/search?beacon=cytognomix), as well as through our website (https://validsplicemut.cytognomix.com/).

Single nucleotide polymorphisms in candidate genes associated with milk yield in Argentinean Holstein and Holstein x Jersey cows

BackgroundResearch on loci influencing milk production traits of dairy cattle is one of the main topics of investigation in livestock. Many genomic regions and polymorphisms associated with dairy production have been reported worldwide. In this context, the purpose of this study was to identify candidate loci associated with milk yield in Argentinean dairy cattle. A database of candidate genes and single nucleotide polymorphisms (SNPs) for milk production and composition was developed. Thirty-nine SNPs belonging to 22 candidate genes were genotyped on 1643 animals (Holstein and Holstein x Jersey). The genotypes obtained were subjected to association studies considering the whole population and discriminating the population by Holstein breed percentage. Phenotypic data consisted of milk production values recorded during the first lactation of 1156 Holstein and 462 Holstein x Jersey cows from 18 dairy farms located in the central dairy area of Argentina. From these records, 305-day cumulative milk production values were predicted.ResultsEight SNPs (rs43375517, rs29004488, rs132812135, rs137651874, rs109191047, rs135164815, rs43706485, and rs41255693), located on six Bos taurus autosomes (BTA4, BTA6, BTA19, BTA20, BTA22, and BTA26), showed suggestive associations with 305-day cumulative milk production (under Benjamini-Hochberg procedure with a false discovery rate of 0.1). Two of those SNPs (rs43375517 and rs135164815) were significantly associated with milk production (Bonferroni adjusted p-values < 0.05) when considering the Holstein population.ConclusionsThe results obtained are consistent with previously reported associations in other Holstein populations. Furthermore, the SNPs found to influence bovine milk production in this study may be used as possible candidate SNPs for marker-assisted selection programs in Argentinean dairy cattle.

Clinical Impact of Clonal and Subclonal TP53 Mutations in Chronic Lymphocytic Leukemia

▪Introduction. The clinical course of patients with chronic lymphocytic leukemia (CLL) is highly heterogeneous. The deletions/mutations of 17p/TP53 are predictors of chemorefractoriness, and for this reason, in the management algorithm of CLL patients, when present, indicate treatment with with chemo-free regimens also in the context of first-line therapy. Recent studies based on ultra-deep-next generation sequencing (NGS) have shown that TP53 mutations can be present at very low clonal abundance in tumor cell populations, although whether these mutations may have a detrimental clinical impact on disease course is still to be established.Aim. To investigate the presence of clonal and subclonal mutations of TP53 in a large cohort of CLL cases using an ultra-deep NGS strategy, and determined their clinical relevance for patients outcome.Methods. The study includes 590 CLL patients characterized for the deletion at chromosome 17p13 (FISH analysis) and TP53 mutations in samples before treatment. In all cases, analyses were carried out on DNA extracted from nearly pure (>90%) tumor cells. TP53 mutational status was investigated by NGS with an amplicon based strategy. Sequencing reads analysis was made by the Burrows-Wheeler Aligner-MEM algorithm and by SAMtools. Variant calling was performed using the entire pipeline established on the MiSeq Reporter software. Results were expressed as percentage of mutated DNA. The minimal allelic fraction for mutation calling was set at 1%. Synonymous variants and polymorphisms described in the Single Nucleotide Polymorphism Database (dbSNP138) were removed. Outcome variable was overall survival (OS). Clinical correlations were made using Kaplan-Meier plots and log-rank test.Results. FISH and mutational analyses were performed in samples within 2 years from diagnosis in 92% of the cases (Figure 1A). A total of 125 TP53 mutations (Figure 1B) were found in 96 patients (11.7%). Subclonal mutations have similar molecular characteristics as their respective high frequency allele mutations supporting a comparable pathogenic effect (Figure 1B). According to a 15% cutoff of variant allele frequency (VAF), 78 cases were considered clonal and 18 subclonal (Figure 1C) for TP53 mutations (1% < VAF < 15%). In this context, cases with subclonal and clonal TP53 mutations experienced significant shorter OS than TP53 wild-type (wt) cases, without differences between clonal and subclonal cases (Figure 1E). Accordingly, ROC analysis on the same cohort identified a cutoff of >0% for the clinical impact of TP53 mutations (Figure 1E inset). Deletion of chromosome 17p was found in 180 out of 574 patients (31.3%), and using a 10% cutoff, 61 patients presented a percentage of deleted nuclei above the cutoff (Figure 1D). Using only 17p deletion data and considering the above mentioned cutoff, patients with 17p13 deletion ≥10% experienced shorter OS than wt cases, while patients with 17p13 deletion <10% experienced OS superimposable to wt cases (Figure 1F). These data were confirmed by ROC analysis that selected >9% of deleted nuclei as optimal cutoff for OS discrimination (Figure 1F inset). Given the frequent co-occurrence of TP53 mutations with 17p deletions, we also evaluated the impact of isolated TP53 mutations and 17p deletions. By using the ROC cutoffs for the definition of mutated/deleted cases, 466 cases (81.1%) presented no TP53 disruption (TP53 mutations and deletion), 47 cases (8.2%) were TP53 mutated only, 15 cases (2.6%) were 17p deleted only and 46 cases (8.1%) presented a concomitant TP53 mutation and 17p deletion. Kaplan-Meier curves demonstrated comparable significant shorter OS intervals for TP53 mutated and/or deleted CLL cases respect to wt cases, while no differences were observed between these three groups (Figure 1G).Conclusion. By using a highly sensitive NGS approach, we have detected small subclones of TP53 in a relative high proportion of patients. TP53 mutations conferred a significant shorter OS irrespectively of VAF percent, while deletion of chromosome 17p impacted on OS only when detectable in more than 10% of nuclei. These cutoffs, once validated by prospective studies, may be employed in daily practice for the clinical management of CLL patients. DisclosuresZaja:Novartis: Honoraria, Research Funding; Abbvie: Honoraria; Celgene: Honoraria, Research Funding; Amgen: Honoraria; Janssen: Honoraria; Takeda: Honoraria; Sandoz: Honoraria.

Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod.

Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although the fine‐scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data‐synthesis approach, integrating multiple genome‐wide single‐nucleotide polymorphism (SNP) datasets representative of different regions to create a single range‐wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post‐glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.

Molecular Analyses in a Rabbit Model of Craniosynostosis: Likely Exclusion of Known Candidate Genes as the Loci of Origin.

Craniosynostosis (CS) involves the premature fusion of one or more cranial sutures. We work with a naturally occurring rabbit model of CS with an undefined etiology. Known causes of coronal CS were evaluated to identify potential associations with CS in the rabbit. Candidate genes were sequenced in control New Zealand White (NZW) rabbits (n = 4) and synostotic NZW rabbits (n = 4). Variants were identified by alignment using Clustal Omega. Single nucleotide variants (SNVs) were classified according to phenotypic associations and predicted impact on protein structure. Human correlates were identified in the database of single nucleotide polymorphisms (dbSNP). A total of 21 SNVs were identified in the 10 genes examined. Variant classification and inheritance patterns are inconsistent with causality. The genetic basis for disease in the CS rabbit likely involves novel loci and is not associated with known causes of coronal synostosis.

Evaluation of Informative SNPs in Iranian Azeri Population

Introduction: Two of the most important tests used in the forensic genetics are DNA fingerprinting and paternity testing. Short tandem repeats (STRs) are very frequently used in identification. Nevertheless, there are limitations on the use of these markers in identifying badly degraded DNA. In these cases, single nucleotide polymorphisms (SNPs) are used because of their shorter amplicon lengths. Recognition of SNPs of high informativeness is a vital step in preparing a list of suitable SNPs. The present research aimed to determine the maximum informative SNPs to be used for identification in Iranian Azari population. Materials and Methods: Four SNPs developed by the SNPforID Consortium were selected. The allele frequencies of the SNPs were obtained using HRM Analysis on DNA samples taken from 100 different individuals. The SNPs that satisfied the Hardy-Weinberg equilibrium and had heterozygosity of higher than 0.50 and equal allele frequency were selected as SNPs of the maximum informativeness. Results: Two polymorphisms (Rs2107612 and Rs1355366) had equal allele frequencies and heterozygosity of higher than 50 percent. Therefore, these 2 polymorphisms are considered highly informative among the studied Azeri population and can be considered in preparing a list of suitable SNPs. Conclusions: Results of the present study can be used along with other SNPs to increase the identification power for some samples. It can also help preparing a database of suitable SNPs to be used for identification in Azeri population in Iran.

AWESOME: a database of SNPs that affect protein post-translational modifications.

Protein post-translational modifications (PTMs), including phosphorylation, ubiquitination, methylation, acetylation, glycosylation et al, are very important biological processes. PTM changes in some critical genes, which may be induced by base-pair substitution, are shown to affect the risk of diseases. Recently, large-scale exome-wide association studies found that missense single nucleotide polymorphisms (SNPs) play an important role in the susceptibility for complex diseases or traits. One of the functional mechanisms of missense SNPs is that they may affect PTMs and leads to a protein dysfunction and its downstream signaling pathway disorder. Here, we constructed a database named AWESOME (A Website Exhibits SNP On Modification Event, http://www.awesome-hust.com), which is an interactive web-based analysis tool that systematically evaluates the role of SNPs on nearly all kinds of PTMs based on 20 available tools. We also provided a well-designed scoring system to compare the performance of different PTM prediction tools and help users to get a better interpretation of results. Users can search SNPs, genes or position of interest, filter with specific modifications or prediction methods, to get a comprehensive PTM change induced by SNPs. In summary, our database provides a convenient way to detect PTM-related SNPs, which may potentially be pathogenic factors or therapeutic targets.

Whole genome sequencing data for two individuals of Pakistani descent

Here we report next-generation based whole genome sequencing of two individuals (H1 and H2) from a family of Pakistani descent. The genomic DNA was used to prepare paired-end libraries for whole-genome sequencing. Deep sequencing yielded 706.49 and 778.12 million mapped reads corresponding to 70.64 and 77.81 Gb sequence data and 23× and 25× average coverage for H1 and H2, respectively. Notably, a total of 448,544 and 470,683 novel variants, not present in the single nucleotide polymorphism database (dbSNP), were identified in H1 and H2, respectively. Comparative analysis identified 2,415,852 variants common in both genomes including 240,181 variants absent in the dbSNP. Principal component analysis linked the ancestry of both genomes with South Asian populations. In conclusion, we report whole genome sequences of two individuals from a family of Pakistani descent.

New SNP Markers to Identify Culex Complex Species (Diptera: Culicidae) by High-Resolution DNA Melting Analysis

The members from Culex pipiens complex are the primary vector of various arboviruses including West Nile virus and Eastern equine encephalitis in the United States. Within Cx. pipiens complex, there are three biotypes that differ largely in habitat, bloodmeal preference, mating behavior, and overwintering strategy. The three biotypes are Cx. pipiens form molestus (F.) (Diptera: Culicidae), Cx. pipiens f. pipiens (L.) (Diptera: Culicidae), and Cx. pipiens quinquefasciatus (Diptera: Culicidae) (also known as Cx. quinquefasciatus). It is clear that additional genetic markers, molecular markers based on single nucleotide polymorphisms (SNPs), were identified from the Cx. pipiens complex species. Genomic DNA was extracted from adult females of f. pipiens and f. molestus and was amplified by polymerase chain reactions. Thirty out of the 100 primer pairs showed amplification and were used for SNP identification. All thirty genes contained biotype-specific SNPs: 10 were located on the Cx. pipiens complex genetic map from previous genetic studies. We also tested a high-resolution DNA melting analysis as a biotype identification method by examining the SNPs in the two genes (CPIJ005487 and CPIJ002074). Our method provides a high confidence for biotype determination among the three Cx. pipiens complex mosquitoes.Data deposition: NCBI SNP Database (ssSNP accession nos.: ss947848635-ss947848878).

Identification of novel variation in introns three and four of the iduronate-2-sulfatase gene in patients with mucopolysaccharidosis type II

To identify and analyze mutations that occur in introns of the iduronate-2-sulfatase (IDS) gene of patients with mucopolysaccharidosis type II (MPS II) in Indonesia. DNA samples from 6 patients with MPS II and 49 normal individuals were analyzed with direct sequencing of introns three and four. A novel variant was found at the site c.419-132del in intron three and three variants were found at c.507 + 26G>A, c.507 + 29G>A, and c.507 + 63T>G in intron four of the IDS gene. These variations occur in the non-splicing site of the IDS gene in patients with MPS II and normal individuals and do not affect the structure of the IDS gene. Alterations which occur in one site of intron three and three sites of intron four are new variations of the IDS gene found in Indonesian patients. This finding suggests that the IDS gene may show variation in other sites that could be associated with MPS II. These mutations can enrich the single nucleotide polymorphism database for the IDS gene globally. Further genotype studies should be performed to obtain a full profile of the IDS gene in patients with MPS II in Indonesia.

Novel variations in Exon 4 of the iduronate 2-sulfatase gene in six Indonesian patients with mucopolysaccharidosis type II

Mucopolysaccharidosis type II (MPS II) is an X-linked lysosomal storage disorder caused by the inability to produce iduronate 2-sulfatase (IDS). We genotyped exon 4 of the IDS gene in Indonesian patients with MPS II. To detect IDS gene mutations, DNA samples from 6 patients with MPS II and 49 normal individuals were analyzed with direct sequencing of exon 4. One novel mutation (c.489G>A) was identified in four of six patients. Protein analysis of these mutations revealed no amino acid sequence changes (silent mutation). Another 20 variations were found in normal individuals, including missense, nonsense, and silent mutations. The discovery of this novel mutation provides new mutational data for MPS II, whereas the identified variations strengthen the single nucleotide polymorphism database for the IDS gene. These mutation and variation data should be useful for identifying biomarkers for diagnosing MPS II.

Two rare loss-of-function variants in the STAG3 gene leading to primary ovarian insufficiency

Background/AimPrimary ovarian insufficiency (POI) is characterized by primary or secondary amenorrhea, infertility, low estradiol levels, and increased gonadotropin levels. Most cases of POI remain unsolved even after exhaustive investigation. Here, we performed a targeted massively parallel sequencing to identify the genetic diagnosis of primary ovarian insufficiency (POI) in a Brazilian patient. Patient and methodsAn adopted 21-year-old Brazilian woman with isolated POI was selected. A custom SureSelectXT DNA target enrichment panel was designed and sequenced on an Illumina NextSeq 500 sequencer. The variants were confirmed using Sanger sequencing. ResultsTwo rare heterozygous pathogenic variants in the STAG3 gene were identified in our patient. An unpublished 1-bp duplication c.291dupC (p.Asn98Glnfs*2) and one stop codon variant c.1950C > A (p.Tyr650*) were identified in the STAG3 gene. Both undescribed heterozygous variants were absent in the public databases [1000Genomes, Exome Aggregation Consortium (ExAC), National Heart, Lung, and Blood Institute Exome Variant Server (NHLBI/EVS), database of Single Nucleotide Polymorphisms (dbSNP), Genome Aggregation Database (gnomAD)], and Online Archive of Brazilian Mutations (ABraOM) databases. Moreover, neither heterozygous variants were found in 400 alleles from fertile Brazilian women screened by Sanger sequencing. The parents' DNA was not available to segregate these variants. ConclusionOur results suggested that POI is caused by pathogenic compound heterozygous variants in the STAG3 gene, supporting the key role of the STAG3 gene in the etiology of primary ovarian insufficiency.

Assessing the Accuracy of Variant Detection in Cost-Effective Gene Panel Testing by Next-Generation Sequencing

There is significant debate within the diagnostics community regarding the accuracy of variant identification by next-generation sequencing and the necessity of confirmatory testing of detected variants. Because the quality threshold to discriminate false positives depends on the workflow, no regulatory standard regarding this matter has yet been published. The goal of this study was to empirically determine the threshold to perform additional Sanger sequencing and to reduce the experimental cost to a practical level. Using 278 model genes, a hybridization capture-based protocol was examined to meet the clinical requirements of low cost, high efficiency, and high-quality data. To reduce excessive false-positive detection, filtering processes were introduced to remove mismapped reads and strand-biased detection to a published best-practices pipeline. With seven samples from the 1000 Genomes Project, 2750 single-nucleotide polymorphisms and 142 insertions/deletions were identified by our designed workflow. Compared with variants registered in the single nucleotide polymorphism database (dbSNP), a zero false-positive threshold value was determined (quality score>1000). The variants satisfying these criteria accounted for 95.6% of single-nucleotide polymorphisms and 50.7% of insertions/deletions. Except for deletions located within the highly repeated sequences, the workflow achieved 100% sensitivity. The established threshold allowed us to discriminate between convincing variants and those requiring validation, a design that reconciles the competing objectives of cost minimization and quality maximization of clinical gene panel testing.

Infantile neuroaxonal dystrophy caused by PLA2G6 gene mutation in a Chinese patient: A case report.

Infantile neuroaxonal dystrophy (INAD) is a rare neurodegenerative disorder. Phospholipase A2 group VI (PLA2G6) gene mutations have been identified in the majority of individuals with INAD. The present case report is on a Chinese female pediatric patient (age, 18 months) diagnosed with INAD with deafness. To date, only four cases of INAD with hearing loss have been reported, PLA2G6-association has not been investigated. Next-generation DNA sequencing technology was used to identify disease-associated genes and Sanger sequencing was applied to verify the mutation in the patient's pedigree. Two mutations were identified in the PLA2G6 gene: c.1T>C (E2) and c.497 (E4) to c.496 (E4): Insert C. The distribution frequency of those mutations in the Single Nucleotide Polymorphism, HapMap, 1000 Genomes and Exome Aggregation Consortium databases was 0. However, cases of INAD appear to be underreported, particularly those from China. The identification of two mutations in the present study suggests unique PLA2G6 mutations in Chinese patients, and greatly expands on the spectrum of known mutations in INAD patients.

Analysis of All 34 Exons of the SPINK5 Gene in Japanese Atopic Dermatitis Patients.

Lympho-epithelial Kazal-type-related inhibitor (LEKTI) is a large multidomain serine protease inhibitor that is expressed in epidermal keratinocytes. Nonsense mutations of the SPINK5 gene, which codes for LEKTI, cause Netherton syndrome, which is characterized by hair abnormality, ichthyosis, and atopy. A single nucleotide polymorphism (SNP) of SPINK5, p.K420E, is reported to be associated with the pathogenesis of atopic dermatitis (AD). We studied all 34 exons of the SPINK5 gene in Japanese 57 AD patients and 50 normal healthy controls. We detected nine nonsynonymous variants, including p.K420E; these variants had already been registered in the SNP database. Among them, p.R654H (n=1) was found as a heterozygous mutation in the AD patients, but not in the control. No new mutation was detected. We next compared the data of the AD patients with data from the Human Genetic Variation Database provided by Kyoto University; a significant difference was found in the frequency of the p.S368N genotype distribution. PolyPhen-2 and SIFT, two algorithms for predicting the functional effects of amino acid substitutions, showed significant scores for p.R654H. Therefore, R654H might be a risk factor for epidermal barrier dysfunction in some Japanese AD patients.

Screening for Wiskott-Aldrich syndrome by flow cytometry

Screening for Wiskott-Aldrich syndrome by flow cytometry

Neural/Bayes network predictor for inheritable cardiac disease pathogenicity and phenotype

The cardiac muscle sarcomere contains multiple proteins contributing to contraction energy transduction and its regulation during a heartbeat. Inheritable heart disease mutants affect most of them but none more frequently than the ventricular myosin motor and cardiac myosin binding protein c (mybpc3). These co-localizing proteins have mybpc3 playing a regulatory role to the energy transducing motor. Residue substitution and functional domain assignment of each mutation in the protein sequence decides, under the direction of a sensible disease model, phenotype and pathogenicity. The unknown model mechanism is decided here using a method combing neural and Bayes networks. Missense single nucleotide polymorphisms (SNPs) are clues for the disease mechanism summarized in an extensive database collecting mutant sequence location and residue substitution as independent variables that imply the dependent disease phenotype and pathogenicity characteristics in 4 dimensional data points (4ddps). The SNP database contains entries with the majority having one or both dependent data entries unfulfilled. A neural network relating causes (mutant residue location and substitution) and effects (phenotype and pathogenicity) is trained, validated, and optimized using fulfilled 4ddps. It then predicts unfulfilled 4ddps providing the implicit disease model. A discrete Bayes network interprets fulfilled and predicted 4ddps with conditional probabilities for phenotype and pathogenicity given mutation location and residue substitution thus relating the neural network implicit model to explicit features of the motor and mybpc3 sequence and structural domains. Neural/Bayes network forecasting automates disease mechanism modeling by leveraging the world wide human missense SNP database that is in place and expanding.

Functional Characterization of Single Nucleotide Polymorphisms in the TMEM163 Gene

Mucolipidosis type IV (MLIV) is a human lysosomal storage disorder caused by a loss or dysfunctional Mucolipin‐1 (TRPML1) ion channel protein. Abnormal levels of zinc accumulation have been found in the brain tissues of MLIV mouse model and cells from MLIV patients. We previously identified a putative zinc transporter called Transmembrane 163 protein (TMEM163) through a yeast two‐hybrid screen in search of interaction partners for TRPML1. We found both proteins to co‐localize on the plasma membrane and lysosomal compartments, and we proposed that both proteins play a role in intracellular zinc homeostasis. The function of TMEM163 has yet to be fully elucidated; however, it is predicted to have six transmembrane domains (TMD) and recent evidence suggests that it transports zinc. To further study TMEM163's function and how it might be involved in certain human diseases like MLIV, we used the single nucleotide polymorphism database (dbSNP) from the National Center for Biotechnology Information (NCBI) website to investigate specific nucleotide sequence variations within the TMEM163 gene. We identified SNPs that produce amino acid substitution when compared with the wild‐type (WT) TMEM163 protein sequence. We then used bioinformatics to predict the topology of TMEM163 protein, and found that some SNP‐associated amino acid substitutions are located in areas of the protein that could affect post‐translational modification and change its structure and function. Thus, we hypothesize that SNPs that result in amino acid substitution dramatically alters the zinc transport function of TMEM163. To accomplish this project, we performed site‐directed mutagenesis using In‐Fusion homologous recombination cloning technique to systematically replace specific nucleotides corresponding to the SNPs located within or in proximity of N‐ and C‐termini, as well as TMD‐1 to TMD‐6. Upon sequence verification, we tested the effect of each SNP‐associated mutant by transfecting them into cultured HeLa cells. Twenty‐four hours post transfection, the cells were exposed to zinc chloride (100 μM) and assayed for intracellular zinc transport using the zinc specific FluoZin‐3 AM dye. We observed that the SNP‐associated mutants have marked decrease in intracellular zinc fluorescence following exposure to exogenous zinc. These observations indicate that certain SNP‐associated amino acid substitution located within critical areas of TMEM163 protein results in abnormal zinc transport. Our preliminary data suggest that TMEM163 is indeed a zinc transporter. We are currently conducting additional experiments using different zinc specific dyes to support this result. Understanding the nature of TMEM163‐TRPML1 interaction is necessary to further support our findings of cellular zinc dyshomeostasis in MLIV cells.Support or Funding InformationThis work was funded by CSUPERB Research and Development Grant 2016, and partly funded by NIH R15 NS101594This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.