ABCA1 : c.2649A>G

ABCA1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.2649A>Gp.I883M (Ile > Met)substitutionmissense chr9:107586753 (reverse strand)0.21329640

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.21329640 (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
ExAC0.13102486
8737 / 66682		0.47558631
4948 / 10404		0.72039778
6230 / 8648		0.14133204
2330 / 16486		0.23827246
2753 / 11554		0.10235863
677 / 6614		0.21696035
197 / 908		0.21329640
25872 / 121296
ESP 0.13419
1154 / 8600		 0.46414
2045 / 4406		 0.24596
3199 / 13006
1KG
 0.14851
120 / 808		 0.50832
672 / 1322		 0.68651
692 / 1008		 0.13497
132 / 978		 0.22334
155 / 694		 0.08081
16 / 198		 0.35683
1787 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.09890
18 / 182
British
0.40984
50 / 122
African-American
0.63978
119 / 186
Chinese Dai
0.16279
28 / 172
Bengali
0.18085
34 / 188
Colombian
0.19159
41 / 214
Iberian
0.52083
100 / 192
African-Caribbean
0.74272
153 / 206
Han, Beijing
0.16019
33 / 206
Gujarati Indian
0.24219
31 / 128
Mexican, LA
0.15421
33 / 214
Toscani
0.48485
96 / 198
Esan, Nigeria
0.59615
124 / 208
Japanese
0.12255
25 / 204
Indian Telugu
0.29412
50 / 170
Peruvian
0.14141
28 / 198
Utah Europeans
0.53982
122 / 226
Gambian
0.71212
141 / 198
Kinh, Vietnam
0.11458
22 / 192
Punjabi, Lahore
0.19231
40 / 208
Puerto Rican
0.48990
97 / 198
Luhya, Kenya
0.73810
155 / 210
Southern Han
0.11765
24 / 204
Tamil
0.54706
93 / 170
Mende
0.52778
114 / 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 ENST00000374736 NM_005502.3
Protein ENSP00000363868 O95477

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
neutral 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.