HELZ2 : c.6509C>T

HELZ2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.6509C>Tp.T2170M (Thr > Met)substitutionmissense chr20:62193445 (reverse strand)0.18545497

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.18545497 (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
ExAC0.15788520
9583 / 60696		0.03245486
266 / 8196		0.58335367
4780 / 8194		0.23303891
3641 / 15624		0.09216758
1012 / 10980		0.17662683
1064 / 6024		0.18671679
149 / 798		0.18545497
20495 / 110512
ESP 0.14643
1254 / 8564		 0.03632
159 / 4378		 0.10918
1413 / 12942
1KG
 0.15223
123 / 808		 0.00681
9 / 1322		 0.57341
578 / 1008		 0.23620
231 / 978		 0.08501
59 / 694		 0.19192
38 / 198		 0.20727
1038 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.15385
28 / 182
British
0.04098
5 / 122
African-American
0.52151
97 / 186
Chinese Dai
0.28488
49 / 172
Bengali
0.13298
25 / 188
Colombian
0.12150
26 / 214
Iberian
0.01562
3 / 192
African-Caribbean
0.53883
111 / 206
Han, Beijing
0.19417
40 / 206
Gujarati Indian
0.08594
11 / 128
Mexican, LA
0.16355
35 / 214
Toscani
0.00000
0 / 198
Esan, Nigeria
0.63942
133 / 208
Japanese
0.25000
51 / 204
Indian Telugu
0.03529
6 / 170
Peruvian
0.17172
34 / 198
Utah Europeans
0.00000
0 / 226
Gambian
0.56566
112 / 198
Kinh, Vietnam
0.22917
44 / 192
Punjabi, Lahore
0.08173
17 / 208
Puerto Rican
0.00505
1 / 198
Luhya, Kenya
0.59524
125 / 210
Southern Han
0.23039
47 / 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 ENST00000467148 NM_001037335.2
Protein ENSP00000417401 Q9BYK8

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
75% of algorithms have predicted that this variant will adversely affect protein function
damaging moderately conservative probably damaging probably damaging
LRT MutationTaster MutationAssessor FATHMM
deleterious polymorphism (auto) medium impact 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.