SYNE1 : c.12150G>T

SYNE1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.12150G>Tp.K4050N (Lys > Asn)substitutionmissense chr6:152658141 (reverse strand)0.07619222

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.07619222 (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
ExAC0.07378262
4885 / 66208		0.05931221
614 / 10352		0.11257036
960 / 8528		0.09882941
1621 / 16402		0.05938429
679 / 11434		0.05361482
353 / 6584		0.06904232
62 / 898		0.07619222
9174 / 120406
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.07426
60 / 808		 0.07489
99 / 1322		 0.11706
118 / 1008		 0.11145
109 / 978		 0.06196
43 / 694		 0.05051
10 / 198		 0.08766
439 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.07692
14 / 182
British
0.09016
11 / 122
African-American
0.07527
14 / 186
Chinese Dai
0.09884
17 / 172
Bengali
0.10638
20 / 188
Colombian
0.08879
19 / 214
Iberian
0.04688
9 / 192
African-Caribbean
0.11650
24 / 206
Han, Beijing
0.12136
25 / 206
Gujarati Indian
0.04688
6 / 128
Mexican, LA
0.06075
13 / 214
Toscani
0.06566
13 / 198
Esan, Nigeria
0.14423
30 / 208
Japanese
0.12255
25 / 204
Indian Telugu
0.02941
5 / 170
Peruvian
0.07071
14 / 198
Utah Europeans
0.10177
23 / 226
Gambian
0.10606
21 / 198
Kinh, Vietnam
0.09375
18 / 192
Punjabi, Lahore
0.05769
12 / 208
Puerto Rican
0.05051
10 / 198
Luhya, Kenya
0.13810
29 / 210
Southern Han
0.11765
24 / 204
Tamil
0.09412
16 / 170
Mende
0.07870
17 / 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 moderately 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.