GATA5 : c.199A>C

GATA5 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.199A>Cp.T67P (Thr > Pro)substitutionmissense chr20:61050379 (reverse strand)0.25641026

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.25641026 (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
ExAC0.24074074
13 / 54		0.20000000
2 / 10		0.00000000
0 / 0		0.35714286
5 / 14		0.00000000
0 / 0		0.00000000
0 / 0		0.00000000
0 / 0		0.25641026
20 / 78
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.15594
126 / 808		 0.07337
97 / 1322		 0.10417
105 / 1008		 0.22393
219 / 978		 0.18876
131 / 694		 0.18182
36 / 198		 0.14257
714 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.12088
22 / 182
British
0.13115
16 / 122
African-American
0.08065
15 / 186
Chinese Dai
0.16860
29 / 172
Bengali
0.20213
38 / 188
Colombian
0.16355
35 / 214
Iberian
0.10938
21 / 192
African-Caribbean
0.11650
24 / 206
Han, Beijing
0.16505
34 / 206
Gujarati Indian
0.17969
23 / 128
Mexican, LA
0.16355
35 / 214
Toscani
0.07071
14 / 198
Esan, Nigeria
0.07692
16 / 208
Japanese
0.21569
44 / 204
Indian Telugu
0.22353
38 / 170
Peruvian
0.17172
34 / 198
Utah Europeans
0.04867
11 / 226
Gambian
0.13131
26 / 198
Kinh, Vietnam
0.29688
57 / 192
Punjabi, Lahore
0.15385
32 / 208
Puerto Rican
0.04545
9 / 198
Luhya, Kenya
0.11429
24 / 210
Southern Han
0.26961
55 / 204
Tamil
0.04118
7 / 170
Mende
0.08796
19 / 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 ENST00000252997 NM_080473.4
Protein ENSP00000252997 Q9BWX5

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 conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
polymorphism (auto) 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.