SYNE1 : c.26060G>A

SYNE1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.26060G>Ap.R8687Q (Arg > Gln)substitutionmissense chr6:152443761 (reverse strand)0.05089692

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.05089692 (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
ExAC0.03859996
2574 / 66684		0.04918981
510 / 10368		0.05807497
502 / 8644		0.06534641
1079 / 16512		0.08596855
995 / 11574		0.07000302
463 / 6614		0.05616740
51 / 908		0.05089692
6174 / 121304
ESP 0.03349
288 / 8600		 0.04063
179 / 4406		 0.03591
467 / 13006
1KG
 0.03218
26 / 808		 0.06430
85 / 1322		 0.07440
75 / 1008		 0.07873
77 / 978		 0.06196
43 / 694		 0.09596
19 / 198		 0.06490
325 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.02198
4 / 182
British
0.04098
5 / 122
African-American
0.08602
16 / 186
Chinese Dai
0.10465
18 / 172
Bengali
0.04255
8 / 188
Colombian
0.03738
8 / 214
Iberian
0.07292
14 / 192
African-Caribbean
0.08738
18 / 206
Han, Beijing
0.06796
14 / 206
Gujarati Indian
0.08594
11 / 128
Mexican, LA
0.02804
6 / 214
Toscani
0.04040
8 / 198
Esan, Nigeria
0.05769
12 / 208
Japanese
0.07843
16 / 204
Indian Telugu
0.10000
17 / 170
Peruvian
0.04040
8 / 198
Utah Europeans
0.09292
21 / 226
Gambian
0.09596
19 / 198
Kinh, Vietnam
0.06250
12 / 192
Punjabi, Lahore
0.03365
7 / 208
Puerto Rican
0.03030
6 / 198
Luhya, Kenya
0.04762
10 / 210
Southern Han
0.08333
17 / 204
Tamil
0.12353
21 / 170
Mende
0.04630
10 / 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 ENST00000423061 LRG_427t2NM_033071.3
Protein ENSP00000396024 LRG_427p2

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 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.