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.339T>C (p.Cys113=)

CA10539080

285094 (ClinVar)

Gene: MTM1
Condition: centronuclear myopathy
Inheritance Mode: X-linked inheritance
UUID: 8fc253b7-3065-4ac1-a409-7f46aec90cde
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_000252.3:c.339T>C
NM_000252.3(MTM1):c.339T>C (p.Cys113=)
NC_000023.11:g.150614696T>C
CM000685.2:g.150614696T>C
NC_000023.10:g.149783169T>C
CM000685.1:g.149783169T>C
NC_000023.9:g.149533827T>C
NG_008199.1:g.51123T>C
ENST00000684910.1:c.136+18126T>C
ENST00000685439.1:c.-3-4342T>C
ENST00000685944.1:c.339T>C
ENST00000687215.1:c.54T>C
ENST00000687365.1:n.394T>C
ENST00000688152.1:c.339T>C
ENST00000688403.1:c.-300-24247T>C
ENST00000689314.1:c.384T>C
ENST00000689694.1:c.339T>C
ENST00000689810.1:c.339T>C
ENST00000690282.1:c.-300-24247T>C
ENST00000690351.1:c.137-4342T>C
ENST00000691232.1:c.-3-4342T>C
ENST00000691686.1:c.339T>C
ENST00000691851.1:c.339T>C
ENST00000692015.1:c.231+16010T>C
ENST00000692638.1:c.*88T>C
ENST00000692852.1:c.339T>C
ENST00000692915.1:c.*334T>C
ENST00000370396.7:c.339T>C
ENST00000306167.11:n.260-4392T>C
ENST00000370396.6:c.339T>C
ENST00000424519.1:c.231+16010T>C
ENST00000490530.1:n.278T>C
NM_000252.2:c.339T>C
NM_001376906.1:c.339T>C
NM_001376907.1:c.232-4342T>C
NM_001376908.1:c.339T>C
More

Benign

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

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.339T>C in MTM1 is a synonymous (silent) variant (p.Cys113=). The highest population filtering allele frequency in gnomAD v4.1.0 is 0.003242 (198/54107 alleles, 58 hemizygotes) in African/African American population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (≥0.000016) for BA1, and therefore meets this criterion (BA1). In addition, SpliceAI does not predict impact to splicing, and the variant occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser (BP4, BP7). 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, BP4, BP7. (Congenital Myopathies VCEP specifications version 1; 8/7/2024)
Met criteria codes
BP7
The c.339T>C (p.Cys113=) variant is a synonymous (silent) variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser
BP4
The c.339T>C (p.Cys113=) variant is a synonymous (silent) variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser
BA1
The highest population filtering allele frequency in gnomAD v4.1.0 is 0.003242 (198/54107 alleles, 58 hemizygotes) in African/African American population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (≥0.000016) for BA1, and therefore meets this criterion
Not Met criteria codes
PM2
The highest population filtering allele frequency in gnomAD v4.1.0 is 0.003242 (198/54107 alleles, 58 hemizygotes) in African/African American population
BS1
The highest population filtering allele frequency in gnomAD v4.1.0 is 0.003242 (198/54107 alleles, 58 hemizygotes) in African/African American population
PP3
The c.339T>C (p.Cys113=) variant is a synonymous (silent) variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser
Curation History
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