APOA4 : c.1099A>T

APOA4 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1099A>Tp.T367S (Thr > Ser)substitutionmissense chr11:116691675 (reverse strand)0.15043386

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.15043386 (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
ExAC0.19389838
12921 / 66638		0.11612469
1207 / 10394		0.00080944
7 / 8648		0.12415172
2049 / 16504		0.08470466
978 / 11546		0.13941871
921 / 6606		0.17222222
155 / 900		0.15043386
18238 / 121236
ESP 0.19718
1693 / 8586		 0.11268
496 / 4402		 0.16854
2189 / 12988
1KG
 0.19207
155 / 807		 0.09235
122 / 1321		 0.00000
0 / 1008		 0.11759
115 / 978		 0.11239
78 / 694		 0.12626
25 / 198		 0.09888
495 / 5006
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.19780
36 / 182
British
0.08197
10 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.08721
15 / 172
Bengali
0.14894
28 / 188
Colombian
0.17757
38 / 214
Iberian
0.13021
25 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.15049
31 / 206
Gujarati Indian
0.13281
17 / 128
Mexican, LA
0.18692
40 / 214
Toscani
0.06566
13 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.10294
21 / 204
Indian Telugu
0.04118
7 / 170
Peruvian
0.20812
41 / 197
Utah Europeans
0.11062
25 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.17188
33 / 192
Punjabi, Lahore
0.12500
26 / 208
Puerto Rican
0.05076
10 / 197
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.07353
15 / 204
Tamil
0.08235
14 / 170
Mende
0.11574
25 / 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 ENST00000357780 NM_000482.3
Protein ENSP00000350425

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 (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.