SYNE1 : c.26077C>A

SYNE1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.26077C>Ap.L8693M (Leu > Met)substitutionmissense chr6:152443744 (reverse strand)0.11816429

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.11816429 (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
ExAC0.15163689
10116 / 66712		0.02850539
296 / 10384		0.05946321
514 / 8644		0.08908672
1471 / 16512		0.04294107
497 / 11574		0.20169338
1334 / 6614		0.12224670
111 / 908		0.11816429
14339 / 121348
ESP 0.13977
1202 / 8600		 0.03450
152 / 4406		 0.10411
1354 / 13006
1KG
 0.12871
104 / 808		 0.02042
27 / 1322		 0.06746
68 / 1008		 0.10532
103 / 978		 0.05331
37 / 694		 0.23232
46 / 198		 0.07688
385 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.15934
29 / 182
British
0.04918
6 / 122
African-American
0.04839
9 / 186
Chinese Dai
0.09884
17 / 172
Bengali
0.07979
15 / 188
Colombian
0.07477
16 / 214
Iberian
0.02604
5 / 192
African-Caribbean
0.07282
15 / 206
Han, Beijing
0.11650
24 / 206
Gujarati Indian
0.04688
6 / 128
Mexican, LA
0.11682
25 / 214
Toscani
0.01010
2 / 198
Esan, Nigeria
0.10577
22 / 208
Japanese
0.09804
20 / 204
Indian Telugu
0.03529
6 / 170
Peruvian
0.17172
34 / 198
Utah Europeans
0.00885
2 / 226
Gambian
0.05556
11 / 198
Kinh, Vietnam
0.09375
18 / 192
Punjabi, Lahore
0.04808
10 / 208
Puerto Rican
0.03535
7 / 198
Luhya, Kenya
0.05238
11 / 210
Southern Han
0.11765
24 / 204
Tamil
0.00588
1 / 170
Mende
0.01852
4 / 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
50% of algorithms have predicted that this variant will adversely affect protein function
damaging conservative probably damaging probably damaging
LRT MutationTaster MutationAssessor FATHMM
neutral 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.