SCN5A : c.1673A>G

SCN5A gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1673A>Gp.H558R (His > Arg)substitutionmissense chr3:38645420 (reverse strand)0.22173617

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.22173617 (ExAC mean allelic frequency), it is highly unlikely to be pathogenic.

DCM

OMGL: Detected in 0 / 304 DCM patients.

For more information on the clinical significance of this variant, please see the ClinVar entry.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.22460327
14946 / 66544		0.28796240
2818 / 9786		0.09925616
854 / 8604		0.24833394
4099 / 16506		0.21388937
2467 / 11534		0.20239177
1337 / 6606		0.21524664
192 / 892		0.22173617
26713 / 120472
ESP 0.23209
1957 / 8432		 0.27483
1151 / 4188		 0.24628
3108 / 12620
1KG
 0.22649
183 / 808		 0.30938
409 / 1322		 0.10119
102 / 1008		 0.27301
267 / 978		 0.22767
158 / 694		 0.17677
35 / 198		 0.23043
1154 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.22527
41 / 182
British
0.26230
32 / 122
African-American
0.06989
13 / 186
Chinese Dai
0.27907
48 / 172
Bengali
0.23936
45 / 188
Colombian
0.26168
56 / 214
Iberian
0.28125
54 / 192
African-Caribbean
0.12621
26 / 206
Han, Beijing
0.20388
42 / 206
Gujarati Indian
0.16406
21 / 128
Mexican, LA
0.23364
50 / 214
Toscani
0.21717
43 / 198
Esan, Nigeria
0.13462
28 / 208
Japanese
0.29412
60 / 204
Indian Telugu
0.22353
38 / 170
Peruvian
0.18182
36 / 198
Utah Europeans
0.37168
84 / 226
Gambian
0.07576
15 / 198
Kinh, Vietnam
0.26042
50 / 192
Punjabi, Lahore
0.25962
54 / 208
Puerto Rican
0.30303
60 / 198
Luhya, Kenya
0.09524
20 / 210
Southern Han
0.32843
67 / 204
Tamil
0.38235
65 / 170
Mende
0.32870
71 / 216
Yoruba, Nigeria

The Exome Aggregation Consortium (ExAC) is a database of 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. There is partial overlap between ExAC and 1000 Genomes (1KG) (1,851 of the 2,504 samples in 1KG) and the Exome Sequencing Project (ESP) (3,936 of the 6,500 samples in ESP).


Other Variant & Gene Details

Canonical Sequences
Transcript ENST00000333535 LRG_289t1NM_198056.2
Protein ENSP00000328968 LRG_289p1Q14524

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
12.5% of algorithms have predicted that this variant will adversely affect protein function
tolerated conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism (auto) neutral damaging


References

1. Roddy Walsh, Kate L. Thomson, James S. Ware, Birgit H. Funke, Jessica Woodley, Karen J. McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C. Taylor, Eric V. Minikel, Exome Aggregation Consortium, Daniel G. MacArthur, Martin Farrall, Stuart A. Cook and Hugh Watkins. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2016 doi:10.1038/gim.2016.90.

2. Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, Seidman MA, Baxter SM, Bowser M, Harrison B, Aaron D, Mahanta LM, Lakdawala NK, McDermott G, White ET, Rehm HL, Lebo M, Funke BH. The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. Genet Med. 2014 Aug;16(8):601-8.

3. Alfares AA, Kelly MA, McDermott G, Funke BH, Lebo MS, Baxter SB, Shen J, McLaughlin HM, Clark EH, Babb LJ, Cox SW, DePalma SR, Ho CY, Seidman JG, Seidman CE, Rehm HL. Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. Genet Med. 2015 Nov;17(11):880-8.