PKP2 : c.1636G>A

PKP2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1636G>Ap.A546T (Ala > Thr)substitutionmissense chr12:32994014 (reverse strand)0.00021417

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.00021417 (ExAC mean allelic frequency), it is unlikely to be pathogenic.

DCM

OMGL: Detected in 0 / 304 DCM patients.

LMM:   Detected in 0 / 123 DCM patients.

ARVC

OMGL: Detected in 0 / 361 ARVC patients sequenced at OMGL.

For more information on the clinical significance of this variant, please see the ClinVar entry.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.00000000
0 / 66734		0.00009612
1 / 10404		0.00000000
0 / 8652		0.00000000
0 / 16510		0.00215927
25 / 11578		0.00000000
0 / 6614		0.00000000
0 / 908		0.00021417
26 / 121400
ESP 0.00012
1 / 8600		 0.00000
0 / 4406		 0.00008
1 / 13006
1KG
 0.00000
0 / 1006		 0.00000
0 / 1322		 0.00000
0 / 1008		 0.00000
0 / 978		 0.00432
3 / 694		 0.00000
0 / 198		 0.00060
3 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.00000
0 / 182
British
0.00000
0 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.00000
0 / 172
Bengali
0.00532
1 / 188
Colombian
0.00000
0 / 214
Iberian
0.00000
0 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.00000
0 / 206
Gujarati Indian
0.00000
0 / 128
Mexican, LA
0.00000
0 / 214
Toscani
0.00000
0 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.00000
0 / 204
Indian Telugu
0.00588
1 / 170
Peruvian
0.00000
0 / 198
Utah Europeans
0.00000
0 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.00000
0 / 192
Punjabi, Lahore
0.00481
1 / 208
Puerto Rican
0.00000
0 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.00000
0 / 204
Tamil
0.00000
0 / 170
Mende
0.00000
0 / 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 ENST00000070846 LRG_398t1NM_004572.3
Protein ENSP00000070846 LRG_398p1Q99959

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
12.5% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately conservative possibly damaging benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism 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.