PRDM16 : c.1898C>T

PRDM16 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1898C>Tp.P633L (Pro > Leu)substitutionmissense chr1:3328659 (forward strand)0.13102870

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.13102870 (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
ExAC0.16359979
10491 / 64126		0.16983523
1608 / 9468		0.01083883
92 / 8488		0.08394578
1028 / 12246		0.07366771
846 / 11484		0.09712557
642 / 6610		0.15942029
132 / 828		0.13102870
14839 / 113250
ESP 0.15158
1283 / 8464		 0.15376
659 / 4286		 0.15231
1942 / 12750
1KG
 0.17698
143 / 808		 0.16339
216 / 1322		 0.00595
6 / 1008		 0.05930
58 / 978		 0.12104
84 / 694		 0.12121
24 / 198		 0.10603
531 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.10989
20 / 182
British
0.16393
20 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.05233
9 / 172
Bengali
0.19149
36 / 188
Colombian
0.19626
42 / 214
Iberian
0.12500
24 / 192
African-Caribbean
0.00485
1 / 206
Han, Beijing
0.05825
12 / 206
Gujarati Indian
0.10156
13 / 128
Mexican, LA
0.22430
48 / 214
Toscani
0.19192
38 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.03922
8 / 204
Indian Telugu
0.04706
8 / 170
Peruvian
0.16667
33 / 198
Utah Europeans
0.15487
35 / 226
Gambian
0.01010
2 / 198
Kinh, Vietnam
0.07292
14 / 192
Punjabi, Lahore
0.12981
27 / 208
Puerto Rican
0.18182
36 / 198
Luhya, Kenya
0.01429
3 / 210
Southern Han
0.07353
15 / 204
Tamil
0.20000
34 / 170
Mende
0.13426
29 / 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 ENST00000270722 NM_022114.3
Protein ENSP00000270722 Q9HAZ2

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.