SCARB1 : c.4G>A

SCARB1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.4G>Ap.G2S (Gly > Ser)substitutionmissense chr12:125348263 (reverse strand)0.10841664

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.10841664 (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
ExAC0.16868576
919 / 5448		0.08872180
118 / 1330		0.00000000
0 / 348		0.06896552
496 / 7192		0.17777778
48 / 270		0.08823529
6 / 68		0.12162162
18 / 148		0.10841664
1605 / 14804
ESP 0.09913
800 / 8070		 0.05249
221 / 4210		 0.08314
1021 / 12280
1KG
 0.12871
104 / 808		 0.06657
88 / 1322		 0.00298
3 / 1008		 0.04601
45 / 978		 0.09942
69 / 694		 0.06566
13 / 198		 0.06430
322 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.09341
17 / 182
British
0.09836
12 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.02907
5 / 172
Bengali
0.09043
17 / 188
Colombian
0.14019
30 / 214
Iberian
0.06250
12 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.03883
8 / 206
Gujarati Indian
0.08594
11 / 128
Mexican, LA
0.18224
39 / 214
Toscani
0.05051
10 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.06373
13 / 204
Indian Telugu
0.05882
10 / 170
Peruvian
0.09091
18 / 198
Utah Europeans
0.05310
12 / 226
Gambian
0.01515
3 / 198
Kinh, Vietnam
0.04688
9 / 192
Punjabi, Lahore
0.14904
31 / 208
Puerto Rican
0.11111
22 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.04902
10 / 204
Tamil
0.03529
6 / 170
Mende
0.06481
14 / 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 ENST00000261693 NM_005505.4
Protein ENSP00000261693

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
37.5% of algorithms have predicted that this variant will adversely affect protein function
damaging moderately conservative probably damaging probably damaging
LRT MutationTaster MutationAssessor FATHMM
unknown polymorphism (auto) low impact 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.