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
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Variant: NM_000252.3(MTM1):c.141_144del

CA255668

11057 (ClinVar)

Gene: MTM1
Condition: centronuclear myopathy
Inheritance Mode: X-linked inheritance
UUID: fa05e62c-7632-4ef7-856e-5304d55f8d85
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_000252.3:c.141_144del
NM_000252.3(MTM1):c.141_144del
NC_000023.11:g.150598596_150598599del
CM000685.2:g.150598596_150598599del
NC_000023.10:g.149767060_149767063del
CM000685.1:g.149767060_149767063del
NC_000023.9:g.149517718_149517721del
NG_008199.1:g.35014_35017del
ENST00000684910.1:c.136+2026_136+2029del
ENST00000685439.1:c.-3-20442_-3-20439del
ENST00000685944.1:c.141_144del
ENST00000687215.1:c.-145_-142del
ENST00000687365.1:n.196_199del
ENST00000688152.1:c.141_144del
ENST00000688403.1:c.-301+29734_-301+29737del
ENST00000689314.1:c.141_144del
ENST00000689694.1:c.141_144del
ENST00000689810.1:c.141_144del
ENST00000690282.1:c.-301+29878_-301+29881del
ENST00000690351.1:c.136+2026_136+2029del
ENST00000691232.1:c.-3-20442_-3-20439del
ENST00000691686.1:c.141_144del
ENST00000691851.1:c.141_144del
ENST00000692015.1:c.141_144del
ENST00000692638.1:c.136+2026_136+2029del
ENST00000692852.1:c.141_144del
ENST00000692915.1:c.141_144del
ENST00000693422.1:n.202_205del
ENST00000370396.7:c.141_144del
ENST00000306167.11:n.180_183del
ENST00000370396.6:c.141_144del
ENST00000424519.1:c.141_144del
ENST00000490530.1:n.170+2026_170+2029del
NM_000252.2:c.141_144del
NM_001376906.1:c.141_144del
NM_001376907.1:c.141_144del
NM_001376908.1:c.141_144del
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Pathogenic

Met criteria codes 6
PS4 PP1 PP4 PM6 PM2_Supporting PVS1
Not Met criteria codes 2
BA1 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 c.141_144del (p.Glu48LeufsTer24) variant in MTM1 is a deletion variant predicted to cause a premature stop codon in biologically-relevant-exon 4/15 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The c.141_144del variant has been identified in at least 6 male probands with severe centronuclear myopathy, one of which was de novo with unconfirmed parental relationships, and one severely affected female (PMIDs: 9285787, 30241883, 33062893, 33164942, 10063835) (PS4, PM6). Additionally, the variant segregated with disease in an uncle and a male sibling from two separate families (PMID: 9285787) (PP1). At least one patient with this variant displayed a muscle biopsy consistent with centronuclear myopathy (PMID:33164942) (PP4). In summary, this variant meets the criteria to be classified as pathogenic for X-linked centronuclear myopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PVS1, PS4, PM6, PM2_Supporting, PP1, PP4. (ClinGen Congenital Myopathies VCEP specifications version 1; 8/7/2024)
Met criteria codes
PS4
The c.141_144del variant has been identified in at least 6 male probands with severe centronuclear myopathy, one of which was de novo with unconfirmed parental relationships, and one severely affected female (PMIDs 9285787, 30241883, 33062893, 33164942, 10063835).
PP1
The c.141_144del variant was Identified in 4 individuals with severe centronuclear myopathy and segregated with disease in an uncle and a male sibling from two separate families (PMID: 9285787)
PP4
The c.141_144del variant has been identified in at least 6 male probands with severe centronuclear myopathy, and at least one of these probands had a muscle biopsy that is specific for centronuclear myopathy and MTM1 variants (PMID: 33164942).
PM6
The c.141_144del variant has been identified in at least 6 male probands with severe centronuclear myopathy, one of which was de novo with unconfirmed parental relationships, and one severely affected female (PMIDs 9285787, 30241883, 33062893, 33164942, 10063835).
PM2_Supporting
This variant is absent from gnomAD v4.1.0.
PVS1
The variant is an out of frame deletion that results in a frameshift and termination 24 AA downstream (in exon 4/15)
Not Met criteria codes
BA1
This variant is absent from gnomAD v4.1.0.
BS1
This variant is absent from gnomAD v4.1.0.
Curation History
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