HELZ2 : c.5665A>G

HELZ2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.5665A>Gp.T1889A (Thr > Ala)substitutionmissense chr20:62194510 (reverse strand)0.05979219

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.05979219 (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
ExAC0.05421027
1585 / 29238		0.25101317
991 / 3948		0.00161900
6 / 3706		0.00829994
87 / 10482		0.03211716
125 / 3892		0.21912114
369 / 1684		0.06793478
25 / 368		0.05979219
3188 / 53318
ESP 0.02763
232 / 8396		 0.15229
653 / 4288		 0.06977
885 / 12684
1KG
 0.03218
26 / 808		 0.19289
255 / 1322		 0.00198
2 / 1008		 0.00409
4 / 978		 0.04755
33 / 694		 0.12121
24 / 198		 0.06869
344 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.01648
3 / 182
British
0.14754
18 / 122
African-American
0.00538
1 / 186
Chinese Dai
0.01163
2 / 172
Bengali
0.06383
12 / 188
Colombian
0.04206
9 / 214
Iberian
0.20833
40 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.00000
0 / 206
Gujarati Indian
0.02344
3 / 128
Mexican, LA
0.03738
8 / 214
Toscani
0.21717
43 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.00000
0 / 204
Indian Telugu
0.01176
2 / 170
Peruvian
0.03030
6 / 198
Utah Europeans
0.24336
55 / 226
Gambian
0.00505
1 / 198
Kinh, Vietnam
0.00000
0 / 192
Punjabi, Lahore
0.07692
16 / 208
Puerto Rican
0.18182
36 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.00980
2 / 204
Tamil
0.21176
36 / 170
Mende
0.12500
27 / 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
0% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism 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.