WNK1 : c.3489+4C>T

WNK1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.3489+4C>Tsubstitutionsplice site chr12:992229 (forward strand)0.11832935

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.11832935 (ExAC mean allelic frequency), it is highly unlikely to be pathogenic.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.13477101
8993 / 66728		0.04646018
483 / 10396		0.08134966
704 / 8654		0.17217781
2843 / 16512		0.05259976
609 / 11578		0.09495011
628 / 6614		0.11453744
104 / 908		0.11832935
14364 / 121390
ESP 0.13907
1196 / 8600		 0.04675
206 / 4406		 0.10780
1402 / 13006
1KG
 0.13861
112 / 808		 0.03555
47 / 1322		 0.10913
110 / 1008		 0.16667
163 / 978		 0.07925
55 / 694		 0.09596
19 / 198		 0.10104
506 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.12088
22 / 182
British
0.03279
4 / 122
African-American
0.09677
18 / 186
Chinese Dai
0.15116
26 / 172
Bengali
0.09574
18 / 188
Colombian
0.13084
28 / 214
Iberian
0.04688
9 / 192
African-Caribbean
0.06311
13 / 206
Han, Beijing
0.19903
41 / 206
Gujarati Indian
0.06250
8 / 128
Mexican, LA
0.18224
39 / 214
Toscani
0.03030
6 / 198
Esan, Nigeria
0.14423
30 / 208
Japanese
0.16667
34 / 204
Indian Telugu
0.02941
5 / 170
Peruvian
0.11616
23 / 198
Utah Europeans
0.03540
8 / 226
Gambian
0.13636
27 / 198
Kinh, Vietnam
0.16667
32 / 192
Punjabi, Lahore
0.11538
24 / 208
Puerto Rican
0.04545
9 / 198
Luhya, Kenya
0.10476
22 / 210
Southern Han
0.14706
30 / 204
Tamil
0.02353
4 / 170
Mende
0.03241
7 / 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 ENST00000315939 NM_018979.3
Protein ENSP00000313059 Q9H4A3



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.