Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_000252.3(MTM1):c.1702A>G (p.Ile568Val)

CA172597

158952 (ClinVar)

Gene: MTM1

Condition: centronuclear myopathy

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 5c169121-a727-4b2c-a0eb-e87c79ebb875

Approved on: 2024-08-07

Published on: 2024-10-01

HGVS expressions

NM_000252.3:c.1702A>G

NM_000252.3(MTM1):c.1702A>G (p.Ile568Val)

NC_000023.11:g.150671485A>G

CM000685.2:g.150671485A>G

NC_000023.10:g.149839958A>G

CM000685.1:g.149839958A>G

NC_000023.9:g.149590616A>G

NG_008199.1:g.107912A>G

ENST00000684910.1:c.*1235A>G

ENST00000685439.1:c.1357A>G

ENST00000685944.1:c.1702A>G

ENST00000686212.1:n.1304A>G

ENST00000687215.1:c.*1457A>G

ENST00000688152.1:c.*1146A>G

ENST00000688403.1:c.958A>G

ENST00000689314.1:c.1747A>G

ENST00000689694.1:c.1702A>G

ENST00000689810.1:c.*1351A>G

ENST00000690282.1:c.958A>G

ENST00000690351.1:c.*1354A>G

ENST00000691232.1:c.1357A>G

ENST00000691482.1:n.5665A>G

ENST00000691686.1:c.1609A>G

ENST00000691851.1:c.1111A>G

ENST00000692015.1:c.1489A>G

ENST00000692638.1:c.*1500A>G

ENST00000692852.1:c.1513A>G

ENST00000692915.1:c.*1848A>G

ENST00000370396.7:c.1702A>G

ENST00000306167.11:n.1566A>G

ENST00000370396.6:c.1702A>G

NM_000252.2:c.1702A>G

NM_001376906.1:c.1699A>G

NM_001376907.1:c.1591A>G

NM_001376908.1:c.1702A>G

Benign

BA1

BP4 PP3 PM2 BS1

Evidence Links 0

Expert Panel

Congenital Myopathies VCEP

Criteria Specification Information

Criteria Specification: ClinGen Congenital Myopathies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MTM1 Version 1.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Congenital Myopathies VCEP

The c.1702A>G variant in MTM1 is a missense variant predicted to cause substitution of isoleucine by valine at amino acid 568. The highest population filtering allele frequency in gnomAD v4.1.0 is 0.00002629 (33/895101 alleles, 9 hemizygotes) in European (non-Finnish) population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (≥0.000016) for BA1, and therefore meets this criterion (BA1). The computational predictor REVEL gives a score of 0.212, which is neither above nor below the thresholds predicting a damaging or benign impact on MTM1 function. In summary, this variant meets the criteria to be classified as benign for X-linked centronuclear myopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: BA1. (Congenital Myopathies VCEP specifications version 1; 8/7/2024)

BA1

The highest population filtering allele frequency in gnomAD v4.1.0 is 0.00002629 (33/895101 alleles, 9 hemizygotes) in European (non-Finnish) population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (≥0.000016) for BA1, and therefore meets this criterion

BP4

The computational predictor REVEL gives a score of 0.212, which is neither above nor below the thresholds predicting a damaging or benign impact on MTM1 function.

PP3

The computational predictor REVEL gives a score of 0.212, which is neither above nor below the thresholds predicting a damaging or benign impact on MTM1 function.

PM2

The highest population filtering allele frequency in gnomAD v4.1.0 is 0.00002629 (33/895101 alleles, 9 hemizygotes) in European (non-Finnish) population

BS1

The highest population filtering allele frequency in gnomAD v4.1.0 is 0.00002629 (33/895101 alleles, 9 hemizygotes) in European (non-Finnish) population

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