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_001005361.3(DNM2):c.1105C>T (p.Arg369Trp)

CA118658

7280 (ClinVar)

Gene: DNM2
Condition: centronuclear myopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 844ac971-8611-43e6-ba41-968eb781c8cc
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_001005361.3:c.1105C>T
NM_001005361.3(DNM2):c.1105C>T (p.Arg369Trp)
NC_000019.10:g.10793832C>T
CM000681.2:g.10793832C>T
NC_000019.9:g.10904508C>T
CM000681.1:g.10904508C>T
NC_000019.8:g.10765508C>T
NG_008792.1:g.80754C>T
ENST00000682285.1:n.1293C>T
ENST00000682524.1:n.1293C>T
ENST00000683738.1:n.1293C>T
ENST00000355667.11:c.1105C>T
ENST00000389253.9:c.1105C>T
ENST00000355667.10:c.1105C>T
ENST00000359692.10:c.1105C>T
ENST00000389253.8:c.1105C>T
ENST00000408974.8:c.1105C>T
ENST00000585892.5:c.1105C>T
ENST00000587830.2:c.361C>T
ENST00000591701.5:n.465C>T
NM_001005360.2:c.1105C>T
NM_001005361.2:c.1105C>T
NM_001005362.2:c.1105C>T
NM_001190716.1:c.1105C>T
NM_004945.3:c.1105C>T
NM_001190716.2:c.1105C>T
NM_001005360.3:c.1105C>T
NM_001005362.3:c.1105C>T
NM_004945.4:c.1105C>T

Pathogenic

Met criteria codes 7
PM5 PM6 PM2_Supporting PS3_Supporting PS4 PP1_Strong PP2
Not Met criteria codes 2
BP4 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 DNM2 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The c.1105C>T variant in DNM2 is a missense variant predicted to cause substitution of arginine by tryptophan at amino acid 369 (p.Arg369Trp). The highest population minor allele frequency in gnomAD v4.1 is 0.00001335 (1/74912 alleles) in the African/African American population, which is lower than the ClinGen Congenital Myopathies VCEP threshold for PM2_Supporting, meeting this criterion (PM2_Supporting). DNM2, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). The computational predictor REVEL gives a score of 0.683, which is neither above nor below the thresholds predicting a damaging or benign impact on RYR1 function. This variant has been reported in at least 11 probands from 6 families meeting phenotypic criteria distal muscular weakness and ptosis, which is highly specific for centronuclear myopathy (PS4; PMIDs: 16227997, 20817456, 22613877, 25492887, 25501959, 28676641). The variant has been reported to segregate with centronuclear myopathy in 5 affected family members from 2 families (PP1_Strong; PMIDs: 16227997, 22613877). Two different missense variants (c.1106G>T, p.Arg369Leu; p.Arg369Gln, c.1106G>A) in the same codon have been classified as likely pathogenic and pathogenic, respectively, for autosomal dominant centronuclear myopathy by the ClinGen Congenital Myopathies VCEP (and autosomal dominant Charcot-Marie-Tooth disease by the ClinGen Charcot-Marie-Tooth disease VCEP) (PM5). This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with centronuclear myopathy (PM6; PMIDs: 16227997). A cell culture of human myoblasts from quadriceps showed impaired actin development, indicating that this variant impacts protein function (PMID: 28676641; PS3_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant centronuclear myopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PS4, PP1_Strong, PM5, PM6, PM2_Supporting, PP2, PS3_Supporting. (ClinGen Congenital Myopathies VCEP specifications version 1; 8/7/24)
Met criteria codes
PM5
2 different missense variants, [c.1106G>T, [p.Arg369Leu; p.Arg369Gln, c.1106G>A ]in the same codon have been classified as [likely pathogenic and pathogenic, respectively] for Autosomal dominant centronuclear myopathy and autosomal dominant Charcot-Marie-Tooth disease by the ClinGen Congenital Myopathies VCEP [PM5].
PM6
This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with centronuclear myopathy (PM6; PMIDs: 16227997).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1 is 0.00001335 (1/74912 alleles) in the African/African American population, which is lower than the ClinGen Congenital Myopathies VCEP threshold for PM2_Supporting, meeting this criterion (PM2_Supporting).
PS3_Supporting
A cell culture of human myoblasts from quadriceps showed impaired actin development, indicating that this variant impacts protein function (PMID: 28676641)(PS3_supporting).
PS4
This variant has been reported in 11 probands from 6 families meeting phenotypic criteria distal muscular weakness, which is highly specific for centro-nuclear myopathy (PS4; PMIDs: 16227997, 20817456, 22613877, 25492887, 25501959, 28676641).
PP1_Strong
The variant has been reported to segregate with centro-nuclear myopathy in 5 affected family members from 2 families (PP1_strong; PMIDs: 16227997, 22613877).
PP2
DNM2, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). The Z-score for missense variants in this gene is 3.48.
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
Variant's REVEL score is 0.683 (just below the threshold of 0.7 for applying PP3). Amino acid is very well conserved, and this change is predicted to be deleterious by most in-silico predictors, including SIFT, PolyPhen2, and LRT.
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