Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000252.3(MTM1):c.582C>T (p.Leu194=)

CA10539132

385140 (ClinVar)

Gene: MTM1
Condition: centronuclear myopathy
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 22a64ad7-c929-4b1c-ab64-14a66e3f11ec
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_000252.3:c.582C>T
NM_000252.3(MTM1):c.582C>T (p.Leu194=)
NC_000023.11:g.150641322C>T
CM000685.2:g.150641322C>T
NC_000023.10:g.149809795C>T
CM000685.1:g.149809795C>T
NC_000023.9:g.149560453C>T
NG_008199.1:g.77749C>T
ENST00000684910.1:c.*115C>T
ENST00000685439.1:c.237C>T
ENST00000685944.1:c.582C>T
ENST00000686212.1:n.184C>T
ENST00000687215.1:c.*337C>T
ENST00000688152.1:c.*26C>T
ENST00000688403.1:c.-163C>T
ENST00000689314.1:c.627C>T
ENST00000689694.1:c.582C>T
ENST00000689810.1:c.*231C>T
ENST00000690282.1:c.-163C>T
ENST00000690351.1:c.*234C>T
ENST00000691232.1:c.237C>T
ENST00000691482.1:n.1597C>T
ENST00000691686.1:c.582C>T
ENST00000691851.1:c.582C>T
ENST00000692015.1:c.369C>T
ENST00000692638.1:c.*387C>T
ENST00000692852.1:c.582C>T
ENST00000692915.1:c.*789C>T
ENST00000370396.7:c.582C>T
ENST00000306167.11:n.449C>T
ENST00000370396.6:c.582C>T
ENST00000490530.1:n.521C>T
NM_000252.2:c.582C>T
NM_001376906.1:c.582C>T
NM_001376907.1:c.471C>T
NM_001376908.1:c.582C>T
More

Benign

Met criteria codes 3
BA1 BP7 BP4
Not Met criteria codes 3
PP3 PM2 BS1

Evidence Links 0

Expert Panel

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 variant NM_000252.3(MTM1):c.582C>T is a synonymous (silent) variant (p.Leu194=). The filtering allele frequency in gnomAD v4.1.0 is 0.002821 (112/33731 alleles, 2 homozygote, 36 hemizygotes) for the East Asian population, which is higher than the ClinGen congenital myopathy MTM1 threshold (≥0.000016) for BA1, and therefore meets this criterion (BA1). In addition, SpliceAI predicted no impact on splicing, meeting BP4/BP7 criteria. In summary, the variant meets criteria to be classified as benign. ACMG/AMP criteria met, as specified by the congenital myopathies VCEP: BA1, BP4, BP7 (ClinGen Congenital Myopathies VCEP specifications version 1; 8/7/2024).
Met criteria codes
BA1
The filtering allele frequency in gnomAD v4.1.0 is 0.002821 (112/33731 alleles, 2 homozygote, 36 hemizygotes) for the East Asian population, which is higher than the ClinGen congenital myopathy MTM1 threshold (≥0.000016) for BA1, and therefore meets this criterion
BP7
SpliceAI predicted no impact on splicing, meeting BP4/BP7 criteria.
BP4
SpliceAI predicted no impact on splicing, meeting BP4/BP7 criteria.
Not Met criteria codes
PP3
SpliceAI predicted no impact on splicing, meeting BP4/BP7 criteria.
PM2
The filtering allele frequency in gnomAD v4.1.0 is 0.002821 (112/33731 alleles, 2 homozygote, 36 hemizygotes) for the East Asian population
BS1
The filtering allele frequency in gnomAD v4.1.0 is 0.002821 (112/33731 alleles, 2 homozygote, 36 hemizygotes) for the East Asian population
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.