LAMP2 : c.773C>T

LAMP2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.773C>Tp.T258I (Thr > Ile)substitutionmissense chrX:119580251 (reverse strand)0.00001140

Effect in Cardiac Disease

This variant is considered a rare variant, with a population frequency of 0.00001140 (ExAC mean allelic frequency).

HCM

There is no significant excess of rare LAMP2 Non-Truncating variants in HCM (details).

OMGL: Detected in 0 / 839 HCM patients.

LMM:   Detected in 0 / 2451 HCM patients.

DCM

There is no significant excess of rare LAMP2 Non-Truncating variants in DCM (details).

OMGL: Detected in 0 / 309 DCM patients.

LMM:   Detected in 0 / 223 DCM patients.

For more information on the clinical significance of this variant, please see the ClinVar entry.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.00000000
0 / 47969		0.00011761
1 / 8503		0.00000000
0 / 6637		0.00000000
0 / 10112		0.00000000
0 / 9313		0.00000000
0 / 4530		0.00000000
0 / 633		0.00001140
1 / 87697
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.00000
0 / 766		 0.00100
1 / 1003		 0.00000
0 / 764		 0.00000
0 / 718		 0.00000
0 / 524		 0.00000
0 / 160		 0.00026
1 / 3775
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.00000
0 / 136
British
0.00000
0 / 96
African-American
0.00000
0 / 142
Chinese Dai
0.00000
0 / 130
Bengali
0.00000
0 / 145
Colombian
0.00000
0 / 160
Iberian
0.00000
0 / 145
African-Caribbean
0.00000
0 / 160
Han, Beijing
0.00000
0 / 150
Gujarati Indian
0.00000
0 / 96
Mexican, LA
0.00000
0 / 161
Toscani
0.00000
0 / 145
Esan, Nigeria
0.00000
0 / 152
Japanese
0.00000
0 / 145
Indian Telugu
0.00000
0 / 129
Peruvian
0.00000
0 / 149
Utah Europeans
0.00000
0 / 171
Gambian
0.00000
0 / 152
Kinh, Vietnam
0.00000
0 / 144
Punjabi, Lahore
0.00000
0 / 154
Puerto Rican
0.00649
1 / 154
Luhya, Kenya
0.00000
0 / 158
Southern Han
0.00000
0 / 149
Tamil
0.00000
0 / 128
Mende
0.00000
0 / 164
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 ENST00000200639 NM_002294.2
Protein ENSP00000200639 P13473

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