PDIA2 : c.857C>T

PDIA2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.857C>Tp.T286M (Thr > Met)substitutionmissense chr16:335373 (forward strand)0.09592040

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.09592040 (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
ExAC0.12491152
8118 / 64990		0.15232485
1448 / 9506		0.01193541
102 / 8546		0.02098540
345 / 16440		0.04030425
461 / 11438		0.12196247
793 / 6502		0.09153318
80 / 874		0.09592040
11347 / 118296
ESP 0.11888
995 / 8370		 0.14444
587 / 4064		 0.12723
1582 / 12434
1KG
 0.11757
95 / 808		 0.16793
222 / 1322		 0.00694
7 / 1008		 0.01943
19 / 978		 0.05620
39 / 694		 0.12121
24 / 198		 0.08107
406 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.14835
27 / 182
British
0.14754
18 / 122
African-American
0.01075
2 / 186
Chinese Dai
0.02326
4 / 172
Bengali
0.06915
13 / 188
Colombian
0.12150
26 / 214
Iberian
0.15625
30 / 192
African-Caribbean
0.01942
4 / 206
Han, Beijing
0.03883
8 / 206
Gujarati Indian
0.03906
5 / 128
Mexican, LA
0.08879
19 / 214
Toscani
0.21717
43 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.01471
3 / 204
Indian Telugu
0.00588
1 / 170
Peruvian
0.11616
23 / 198
Utah Europeans
0.11504
26 / 226
Gambian
0.00505
1 / 198
Kinh, Vietnam
0.00521
1 / 192
Punjabi, Lahore
0.09615
20 / 208
Puerto Rican
0.15152
30 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.01471
3 / 204
Tamil
0.08824
15 / 170
Mende
0.27778
60 / 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
62.5% of algorithms have predicted that this variant will adversely affect protein function
damaging moderately conservative possibly damaging probably damaging
LRT MutationTaster MutationAssessor FATHMM
deleterious polymorphism (auto) medium 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.