NEBL : c.1962T>A

NEBL gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1962T>Ap.N654K (Asn > Lys)substitutionmissense chr10:21112137 (reverse strand)0.06059353

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.06059353 (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
ExAC0.02312388
1500 / 64868		0.20185728
2065 / 10230		0.12310785
1041 / 8456		0.09412918
1536 / 16318		0.07240340
817 / 11284		0.02692308
175 / 6500		0.05518018
49 / 888		0.06059353
7183 / 118544
ESP 0.02244
193 / 8600		 0.19246
848 / 4406		 0.08004
1041 / 13006
1KG
 0.02847
23 / 808		 0.23374
309 / 1322		 0.12202
123 / 1008		 0.11759
115 / 978		 0.06916
48 / 694		 0.03030
6 / 198		 0.12460
624 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.02198
4 / 182
British
0.18852
23 / 122
African-American
0.04301
8 / 186
Chinese Dai
0.15116
26 / 172
Bengali
0.09574
18 / 188
Colombian
0.01869
4 / 214
Iberian
0.17708
34 / 192
African-Caribbean
0.12136
25 / 206
Han, Beijing
0.15049
31 / 206
Gujarati Indian
0.05469
7 / 128
Mexican, LA
0.05140
11 / 214
Toscani
0.21717
43 / 198
Esan, Nigeria
0.19231
40 / 208
Japanese
0.08824
18 / 204
Indian Telugu
0.05882
10 / 170
Peruvian
0.02020
4 / 198
Utah Europeans
0.21239
48 / 226
Gambian
0.11616
23 / 198
Kinh, Vietnam
0.09896
19 / 192
Punjabi, Lahore
0.06250
13 / 208
Puerto Rican
0.34848
69 / 198
Luhya, Kenya
0.12857
27 / 210
Southern Han
0.10294
21 / 204
Tamil
0.22941
39 / 170
Mende
0.24537
53 / 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 ENST00000377122 LRG_411t2NM_006393.2
Protein ENSP00000366326 LRG_411p2O76041

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
12.5% of algorithms have predicted that this variant will adversely affect protein function
moderately conservative benign benign
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.