HELZ2 : c.5462T>G

HELZ2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.5462T>Gp.L1821R (Leu > Arg)substitutionmissense chr20:62194713 (reverse strand)0.26980676

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.26980676 (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
ExAC0.19962687
749 / 3752		0.13428571
47 / 350		0.61904762
234 / 378		0.29494604
2241 / 7598		0.22093023
38 / 172		0.28571429
12 / 42		0.23437500
30 / 128		0.26980676
3351 / 12420
ESP 0.11832
895 / 7564		 0.05306
196 / 3694		 0.09691
1091 / 11258
1KG
 0.19307
156 / 808		 0.05749
76 / 1322		 0.59226
597 / 1008		 0.29243
286 / 978		 0.10231
71 / 694		 0.20202
40 / 198		 0.24481
1226 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.18681
34 / 182
British
0.06557
8 / 122
African-American
0.49462
92 / 186
Chinese Dai
0.33721
58 / 172
Bengali
0.14894
28 / 188
Colombian
0.14486
31 / 214
Iberian
0.09375
18 / 192
African-Caribbean
0.58252
120 / 206
Han, Beijing
0.23301
48 / 206
Gujarati Indian
0.10156
13 / 128
Mexican, LA
0.20561
44 / 214
Toscani
0.03535
7 / 198
Esan, Nigeria
0.66346
138 / 208
Japanese
0.30392
62 / 204
Indian Telugu
0.04706
8 / 170
Peruvian
0.23737
47 / 198
Utah Europeans
0.06637
15 / 226
Gambian
0.59091
117 / 198
Kinh, Vietnam
0.29688
57 / 192
Punjabi, Lahore
0.10577
22 / 208
Puerto Rican
0.02525
5 / 198
Luhya, Kenya
0.61905
130 / 210
Southern Han
0.29902
61 / 204
Tamil
0.04118
7 / 170
Mende
0.07407
16 / 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 ENST00000467148 NM_001037335.2
Protein ENSP00000417401 Q9BYK8

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 radical benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism (auto) neutral tolerated


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.