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.1454C>T (p.Ala485Val)

CA10539261

461696 (ClinVar)

Gene: MTM1
Condition: centronuclear myopathy
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 0b403206-059a-4f74-899d-817bf8b9aeb6
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_000252.3:c.1454C>T
NM_000252.3(MTM1):c.1454C>T (p.Ala485Val)
NC_000023.11:g.150660471C>T
CM000685.2:g.150660471C>T
NC_000023.10:g.149828944C>T
CM000685.1:g.149828944C>T
NC_000023.9:g.149579602C>T
NG_008199.1:g.96898C>T
ENST00000684910.1:c.*987C>T
ENST00000685439.1:c.1109C>T
ENST00000685944.1:c.1454C>T
ENST00000686212.1:n.1056C>T
ENST00000687215.1:c.*1209C>T
ENST00000688152.1:c.*898C>T
ENST00000688403.1:c.710C>T
ENST00000689314.1:c.1499C>T
ENST00000689694.1:c.1454C>T
ENST00000689810.1:c.*1103C>T
ENST00000690282.1:c.710C>T
ENST00000690351.1:c.*1106C>T
ENST00000691232.1:c.1109C>T
ENST00000691482.1:n.2469C>T
ENST00000691686.1:c.1361C>T
ENST00000691851.1:c.1053+10570C>T
ENST00000692015.1:c.1241C>T
ENST00000692638.1:c.*1252C>T
ENST00000692852.1:c.1265C>T
ENST00000692915.1:c.*1600C>T
ENST00000370396.7:c.1454C>T
ENST00000306167.11:n.1321C>T
ENST00000370396.6:c.1454C>T
NM_000252.2:c.1454C>T
NM_001376906.1:c.1454C>T
NM_001376907.1:c.1343C>T
NM_001376908.1:c.1454C>T
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 4
BS1 BP4 PP3 PM2

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:c.1454C>T in MTM1 is a missense variant predicted to cause substitution of alanine by valine at amino acid 485 (p.Ala485Val). The filtering allele frequency in gnomAD v4.1.0 is 0.0005657 (35/45691 alleles, 10 hemizygotes) for the Admixed American population, which is higher than the ClinGen congenital myopathy MTM1 threshold (≥0.000016) for BA1, and therefore meets this criterion (BA1). The REVEL computational prediction analysis tool produced a score of 0.221, which is neither above nor below the thresholds predicting a damaging or benign impact on MTM1 function. In summary, the variant meets criteria to be classified as benign. ACMG/AMP criteria met, as specified by the congenital myopathies VCEP: BA1 (ClinGen Congenital Myopathies VCEP specifications version 1; 8/7/2024)
Met criteria codes
BA1
The filtering allele frequency in gnomAD v4.1.0 is 0.0005657 (35/45691 alleles, 10 hemizygotes) for the Admixed American population, which is higher than the ClinGen congenital myopathy MTM1 threshold (≥0.000016) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
BS1
The filtering allele frequency in gnomAD v4.1.0 is 0.0005657 (35/45691 alleles, 10 hemizygotes) for the Admixed American population
BP4
The REVEL computational prediction analysis tool produced a score of 0.221, which is above the threshold to apply BP4 and below the PP3 threshold.
PP3
The REVEL computational prediction analysis tool produced a score of 0.221, which is above the threshold to apply BP4 and below the PP3 threshold.
PM2
The filtering allele frequency in gnomAD v4.1.0 is 0.0005657 (35/45691 alleles, 10 hemizygotes) for the Admixed American population
Curation History
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