SYNE1 : c.24289G>T

SYNE1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.24289G>Tp.A8097S (Ala > Ser)substitutionmissense chr6:152470752 (reverse strand)0.06772721

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.06772721 (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
ExAC0.05606006
3741 / 66732		0.29230769
3040 / 10400		0.00046221
4 / 8654		0.02785853
460 / 16512		0.05326877
616 / 11564		0.04490475
297 / 6614		0.06938326
63 / 908		0.06772721
8221 / 121384
ESP 0.05477
471 / 8600		 0.28575
1259 / 4406		 0.13302
1730 / 13006
1KG
 0.07302
59 / 808		 0.32829
434 / 1322		 0.00099
1 / 1008		 0.01943
19 / 978		 0.08646
60 / 694		 0.03030
6 / 198		 0.11562
579 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.04945
9 / 182
British
0.24590
30 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.01744
3 / 172
Bengali
0.09574
18 / 188
Colombian
0.10280
22 / 214
Iberian
0.28646
55 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.03398
7 / 206
Gujarati Indian
0.05469
7 / 128
Mexican, LA
0.10280
22 / 214
Toscani
0.30808
61 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.01471
3 / 204
Indian Telugu
0.05294
9 / 170
Peruvian
0.03030
6 / 198
Utah Europeans
0.39823
90 / 226
Gambian
0.00505
1 / 198
Kinh, Vietnam
0.01042
2 / 192
Punjabi, Lahore
0.12500
26 / 208
Puerto Rican
0.27778
55 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.01961
4 / 204
Tamil
0.44706
76 / 170
Mende
0.31019
67 / 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.