EGFR : c.1562G>A

EGFR gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1562G>Ap.R521K (Arg > Lys)substitutionmissense chr7:55229255 (forward strand)0.28696319

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.28696319 (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
ExAC0.26462037
17656 / 66722		0.08813918
917 / 10404		0.53588794
4629 / 8638		0.34371214
5674 / 16508		0.30608365
3542 / 11572		0.32289776
2135 / 6612		0.30176211
274 / 908		0.28696319
34827 / 121364
ESP 0.26105
2245 / 8600		 0.08874
391 / 4406		 0.20268
2636 / 13006
1KG
 0.25000
202 / 808		 0.06430
85 / 1322		 0.52381
528 / 1008		 0.35072
343 / 978		 0.32997
229 / 694		 0.38384
76 / 198		 0.29213
1463 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.24176
44 / 182
British
0.10656
13 / 122
African-American
0.50538
94 / 186
Chinese Dai
0.34302
59 / 172
Bengali
0.34574
65 / 188
Colombian
0.25234
54 / 214
Iberian
0.06771
13 / 192
African-Caribbean
0.46117
95 / 206
Han, Beijing
0.35922
74 / 206
Gujarati Indian
0.31250
40 / 128
Mexican, LA
0.24766
53 / 214
Toscani
0.09596
19 / 198
Esan, Nigeria
0.62019
129 / 208
Japanese
0.34314
70 / 204
Indian Telugu
0.36471
62 / 170
Peruvian
0.25758
51 / 198
Utah Europeans
0.07080
16 / 226
Gambian
0.53030
105 / 198
Kinh, Vietnam
0.36458
70 / 192
Punjabi, Lahore
0.29808
62 / 208
Puerto Rican
0.02020
4 / 198
Luhya, Kenya
0.50000
105 / 210
Southern Han
0.34314
70 / 204
Tamil
0.05294
9 / 170
Mende
0.05093
11 / 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 ENST00000275493 NM_005228.3
Protein ENSP00000275493 P00533

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.