PDIA2 : c.1163G>A

PDIA2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1163G>Ap.R388Q (Arg > Gln)substitutionmissense chr16:336396 (forward strand)0.17317556

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.17317556 (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
ExAC0.20652837
13540 / 65560		0.31480713
3036 / 9644		0.04908118
422 / 8598		0.06607662
1090 / 16496		0.09804092
1131 / 11536		0.19488189
1287 / 6604		0.17832957
158 / 886		0.17317556
20664 / 119324
ESP 0.20352
1679 / 8250		 0.29911
1142 / 3818		 0.23376
2821 / 12068
1KG
 0.18069
146 / 808		 0.34569
457 / 1322		 0.03770
38 / 1008		 0.05828
57 / 978		 0.14553
101 / 694		 0.22727
45 / 198		 0.16853
844 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.21978
40 / 182
British
0.30328
37 / 122
African-American
0.02688
5 / 186
Chinese Dai
0.04651
8 / 172
Bengali
0.16489
31 / 188
Colombian
0.20561
44 / 214
Iberian
0.34375
66 / 192
African-Caribbean
0.02913
6 / 206
Han, Beijing
0.05340
11 / 206
Gujarati Indian
0.08594
11 / 128
Mexican, LA
0.11682
25 / 214
Toscani
0.39394
78 / 198
Esan, Nigeria
0.07212
15 / 208
Japanese
0.05882
12 / 204
Indian Telugu
0.08824
15 / 170
Peruvian
0.18687
37 / 198
Utah Europeans
0.30531
69 / 226
Gambian
0.00505
1 / 198
Kinh, Vietnam
0.06771
13 / 192
Punjabi, Lahore
0.21154
44 / 208
Puerto Rican
0.28283
56 / 198
Luhya, Kenya
0.05238
11 / 210
Southern Han
0.06373
13 / 204
Tamil
0.27059
46 / 170
Mende
0.48611
105 / 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 ENST00000219406 NM_006849.2
Protein ENSP00000219406 Q13087

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
0% of algorithms have predicted that this variant will adversely affect protein function
tolerated 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.