SYNM : c.1060A>T

SYNM gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1060A>Tp.R354W (Arg > Trp)substitutionmissense chr15:99669628 (forward strand)0.11392615

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.11392615 (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
ExAC0.09572457
6381 / 66660		0.09961058
972 / 9758		0.30048803
2586 / 8606		0.14437984
2384 / 16512		0.05571873
645 / 11576		0.10356819
685 / 6614		0.09933036
89 / 896		0.11392615
13742 / 120622
ESP 0.08759
720 / 8220		 0.09707
365 / 3760		 0.09057
1085 / 11980
1KG
 0.10149
82 / 808		 0.10817
143 / 1322		 0.27183
274 / 1008		 0.16973
166 / 978		 0.06916
48 / 694		 0.13131
26 / 198		 0.14756
739 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.08242
15 / 182
British
0.12295
15 / 122
African-American
0.18817
35 / 186
Chinese Dai
0.15116
26 / 172
Bengali
0.04255
8 / 188
Colombian
0.12617
27 / 214
Iberian
0.07292
14 / 192
African-Caribbean
0.27670
57 / 206
Han, Beijing
0.19903
41 / 206
Gujarati Indian
0.07031
9 / 128
Mexican, LA
0.11682
25 / 214
Toscani
0.07071
14 / 198
Esan, Nigeria
0.35577
74 / 208
Japanese
0.12255
25 / 204
Indian Telugu
0.04706
8 / 170
Peruvian
0.07576
15 / 198
Utah Europeans
0.15929
36 / 226
Gambian
0.25758
51 / 198
Kinh, Vietnam
0.16667
32 / 192
Punjabi, Lahore
0.11058
23 / 208
Puerto Rican
0.12626
25 / 198
Luhya, Kenya
0.27143
57 / 210
Southern Han
0.20588
42 / 204
Tamil
0.11176
19 / 170
Mende
0.09259
20 / 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 ENST00000336292 LRG_415t1NM_145728.2
Protein ENSP00000336775 LRG_415p1

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
50% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately radical probably damaging possibly damaging
LRT MutationTaster MutationAssessor FATHMM
polymorphism (auto) damaging


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.