HCN4 : c.107G>A

HCN4 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.107G>Ap.G36E (Gly > Glu)substitutionmissense chr15:73660505 (reverse strand)0.06130711

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.06130711 (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
ExAC0.12223151
585 / 4786		0.02631579
14 / 532		0.00000000
0 / 426		0.02634380
198 / 7516		0.10285714
36 / 350		0.08333333
7 / 84		0.05797101
8 / 138		0.06130711
848 / 13832
ESP 0.05075
378 / 7448		 0.00768
27 / 3514		 0.03695
405 / 10962
1KG
 0.07797
63 / 808		 0.00681
9 / 1322		 0.00000
0 / 1008		 0.01534
15 / 978		 0.04467
31 / 694		 0.03535
7 / 198		 0.02496
125 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.03846
7 / 182
British
0.02459
3 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.01163
2 / 172
Bengali
0.09043
17 / 188
Colombian
0.08411
18 / 214
Iberian
0.01042
2 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.03398
7 / 206
Gujarati Indian
0.02344
3 / 128
Mexican, LA
0.11215
24 / 214
Toscani
0.00000
0 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.00980
2 / 204
Indian Telugu
0.02353
4 / 170
Peruvian
0.07071
14 / 198
Utah Europeans
0.01327
3 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.01042
2 / 192
Punjabi, Lahore
0.03365
7 / 208
Puerto Rican
0.00505
1 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.00980
2 / 204
Tamil
0.00000
0 / 170
Mende
0.00000
0 / 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 ENST00000261917 NM_005477.2
Protein ENSP00000261917 Q9Y3Q4

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 moderately conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
polymorphism 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.