SCN5A : c.1141-3C>A

SCN5A gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1141-3C>Asubstitutionsplice site chr3:38647642 (reverse strand)0.17223422

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.17223422 (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
ExAC0.18470681
12184 / 65964		0.12567793
1205 / 9588		0.09556075
818 / 8560		0.17834085
2928 / 16418		0.18364494
2102 / 11446		0.17922236
1180 / 6584		0.17573696
155 / 882		0.17223422
20572 / 119442
ESP 0.18496
1527 / 8256		 0.12675
489 / 3858		 0.16642
2016 / 12114
1KG
 0.18564
150 / 808		 0.12103
160 / 1322		 0.09722
98 / 1008		 0.19325
189 / 978		 0.18588
129 / 694		 0.15657
31 / 198		 0.15116
757 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.18681
34 / 182
British
0.14754
18 / 122
African-American
0.06989
13 / 186
Chinese Dai
0.21512
37 / 172
Bengali
0.20213
38 / 188
Colombian
0.20561
44 / 214
Iberian
0.11979
23 / 192
African-Caribbean
0.11165
23 / 206
Han, Beijing
0.16505
34 / 206
Gujarati Indian
0.10938
14 / 128
Mexican, LA
0.19626
42 / 214
Toscani
0.09596
19 / 198
Esan, Nigeria
0.13462
28 / 208
Japanese
0.18627
38 / 204
Indian Telugu
0.17647
30 / 170
Peruvian
0.15152
30 / 198
Utah Europeans
0.13274
30 / 226
Gambian
0.07576
15 / 198
Kinh, Vietnam
0.15104
29 / 192
Punjabi, Lahore
0.22596
47 / 208
Puerto Rican
0.06566
13 / 198
Luhya, Kenya
0.09048
19 / 210
Southern Han
0.25000
51 / 204
Tamil
0.12353
21 / 170
Mende
0.16667
36 / 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



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.