LIPI : c.1154G>A

LIPI gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1154G>Ap.G385E (Gly > Glu)substitutionmissense chr21:15524921 (reverse strand)0.07109359

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.07109359 (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
ExAC0.02476204
1384 / 55892		0.00995140
86 / 8642		0.27613388
2277 / 8246		0.09473409
1450 / 15306		0.18884558
2035 / 10776		0.03834760
233 / 6076		0.06553398
54 / 824		0.07109359
7519 / 105762
ESP 0.01943
165 / 8490		 0.00706
31 / 4390		 0.01522
196 / 12880
1KG
 0.01980
16 / 808		 0.00681
9 / 1322		 0.25000
252 / 1008		 0.10327
101 / 978		 0.12968
90 / 694		 0.02020
4 / 198		 0.09425
472 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.02198
4 / 182
British
0.01639
2 / 122
African-American
0.22581
42 / 186
Chinese Dai
0.12209
21 / 172
Bengali
0.10638
20 / 188
Colombian
0.01402
3 / 214
Iberian
0.01042
2 / 192
African-Caribbean
0.24272
50 / 206
Han, Beijing
0.08738
18 / 206
Gujarati Indian
0.16406
21 / 128
Mexican, LA
0.00467
1 / 214
Toscani
0.00000
0 / 198
Esan, Nigeria
0.25962
54 / 208
Japanese
0.08824
18 / 204
Indian Telugu
0.24118
41 / 170
Peruvian
0.04040
8 / 198
Utah Europeans
0.00442
1 / 226
Gambian
0.26768
53 / 198
Kinh, Vietnam
0.09896
19 / 192
Punjabi, Lahore
0.03846
8 / 208
Puerto Rican
0.01010
2 / 198
Luhya, Kenya
0.25238
53 / 210
Southern Han
0.12255
25 / 204
Tamil
0.01176
2 / 170
Mende
0.00000
0 / 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 ENST00000344577 NM_198996.2
Protein ENSP00000343331

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
62.5% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately conservative probably damaging probably damaging
LRT MutationTaster MutationAssessor FATHMM
deleterious polymorphism (auto) medium impact 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.