Variant Annotations
PharmGKB variant annotations provide information about variant-drug pairs based on individual PubMed publications. Each annotation represents information from a single paper and the goal is to report the information that the author states, not an interpretation of the paper. The PMID for supporting PubMed publications is found in the "Evidence" field.
Information presented, including study size, allele frequencies and statistics is taken directly from the publication. However, if the author does not correct p-values in cases of multiple hypotheses, curators may apply a Bonferroni correction. Curators attempt to report study size based on the actual number of participants used for the calculation of the association statistics, so the number may vary slightly from what is reported in the abstract of the paper. OMB Race Category information is derived from the paper and mapped to standardized categories. Category definitions may be found by clicking on the "OMB Race Category" link.
There are 4 annotations for this variant. Register or sign in to see them.
VIP Variant in SCN5A
S1103Y was detected only among African Americans [Articles:15851227, 12193783]. About 13.2% of African Americans carry the Y1103 allele. A small case-control study (123 patients and controls) reported a strong association between the variant allele and susceptibility to a range of arrhythmias in African Americans [Article:12193783]. The incidence of homozygotes was 3/133 SIDS subjects vs. 0/1056 controls; in vitro the variant produced an LQT3-like phenotype on exposure to external acid medium [Article:16453024].
Note: The SCN5A gene is found on the minus chromosomal strand. Please note that for standardization, the PharmGKB presents all allele base pairs on the positive chromosomal strand, therefore the alleles within our variant annotations will differ (in a complementary manner) from those in this VIP summary that are given on the minus strand as reported in the literature.
| Key Publications: | |
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| Phenotype |
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Appendix
3. SCN5A:S1103Y
| Genomic Variant & GenBank ID: | 38,560,911 G>T on NT_022517 |
|---|---|
| mRNA Variant & GenBank ID: | 3499 C>A on NM_000335 (transcript variant 2); 3502 C>A on NM_198056(transcript variant 1) |
| Protein Variant & GenBank ID: | 1102 Ser>Tyr on NP_000326 ; 1103 Ser>Tyr on NP_932173 (the two sequences are for the two wild-type splice variants.) |
| GoldenPath Position: | chr3:38595911 (hg18) |
| DNA Source Containing Homozygous Reference Allele(Coriell Lines): | NA17149 (PA126721864) |
| DNA Source Containing Heterozygous Reference Allele(Coriell Lines): | NA17162 (PA126721782) |
Publications related to rs7626962 at chr3:38620907: 4
| A common cardiac sodium channel variant associated with sudden infant death in African Americans, SCN5A S1103Y. The Journal of clinical investigation. 2006. Plant Leigh D, et al. [Article:16453024@PubMed] | |
| Common human SCN5A polymorphisms have altered electrophysiology when expressed in Q1077 splice variants. Heart rhythm : the official journal of the Heart Rhythm Society. 2005. Tan Bi-Hua, et al. [Article:15992732@PubMed] | |
| Spectrum and prevalence of cardiac sodium channel variants among black, white, Asian, and Hispanic individuals: implications for arrhythmogenic susceptibility and Brugada/long QT syndrome genetic testing. Heart rhythm : the official journal of the Heart Rhythm Society. 2004. Ackerman Michael J, et al. [Article:15851227@PubMed] | |
| Variant of SCN5A sodium channel implicated in risk of cardiac arrhythmia. Science (New York, N.Y.). 2002. Splawski Igor, et al. [Article:12193783@PubMed] |
Cross-References
- UCSC Golden Path:
- chr3:38620907
- dbSNP:
- rs7626962
- HapMap:
- rs7626962
Platform Availability
- Illumina