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_001005361.3(DNM2):c.1567A>G (p.Arg523Gly)

CA233294

158515 (ClinVar)

Gene: DNM2
Condition: centronuclear myopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 18e37a48-2e76-422e-aadd-617adbaabfa1
Approved on: 2025-06-09
Published on: 2025-06-23

HGVS expressions

NM_001005361.3:c.1567A>G
NM_001005361.3(DNM2):c.1567A>G (p.Arg523Gly)
NC_000019.10:g.10812273A>G
CM000681.2:g.10812273A>G
NC_000019.9:g.10922949A>G
CM000681.1:g.10922949A>G
NC_000019.8:g.10783949A>G
NG_008792.1:g.99195A>G
ENST00000681972.1:n.998A>G
ENST00000355667.11:c.1567A>G
ENST00000389253.9:c.1567A>G
ENST00000355667.10:c.1567A>G
ENST00000359692.10:c.1555A>G
ENST00000389253.8:c.1567A>G
ENST00000408974.8:c.1555A>G
ENST00000585892.5:c.1567A>G
ENST00000587830.2:c.841A>G
ENST00000590787.1:n.3066A>G
ENST00000590806.5:n.3755A>G
NM_001005360.2:c.1567A>G
NM_001005361.2:c.1567A>G
NM_001005362.2:c.1555A>G
NM_001190716.1:c.1567A>G
NM_004945.3:c.1555A>G
NM_001190716.2:c.1567A>G
NM_001005360.3:c.1567A>G
NM_001005362.3:c.1555A>G
NM_004945.4:c.1555A>G
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Likely Pathogenic

Met criteria codes 4
PS4 PP3 PP2 PM2_Supporting
Not Met criteria codes 22
BS2 PVS1 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP7 BP5 PS2 PS3 PS1 BA1 PP4 PP1 PM1 PM3 PM4 PM5 PM6

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 NM_001005361.3:c.1567A>G variant in DNM2 is a missense variant predicted to cause substitution of arginine by glycine at amino acid 523 (p.Arg523Gly). The variant is absent from gnomAD v4.1.0 meeting 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. The Z-score in gnomAD v4.1.0 is 4.87 (PP2). The REVEL computational prediction analysis tool gives a score of 0.713, which is above the threshold necessary to apply PP3. This variant has been reported in at least three probands with centronuclear myopathy (PS4; PMIDs: 22396310, 25501959; Genetic Services Laboratory, University of Chicago, ClinVar: SCV000193041.1). In summary, the variant meets the criteria to be classified as likely pathogenic for autosomal dominant centronuclear myopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PS4, PM2_Supporting, PP2, PP3 (ClinGen Congenital Myopathies VCEP specifications version 1.0.0; 6/9/2025).
Met criteria codes
PS4
This variant has been reported in at least three probands with centronuclear myopathy (PMIDs: 22396310, 25501959; Genetic Services Laboratory, University of Chicago, ClinVar: SCV000193041.1).
PP3
The REVEL computational prediction analysis tool gives a score of 0.713
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. The Z-score in gnomAD v4.1.0 is 4.87
PM2_Supporting
The variant is absent from gnomAD v4.1.0 meeting PM2_Supporting.
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The variant is absent from gnomAD v4.1.0 meeting PM2_Supporting.
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
The REVEL computational prediction analysis tool gives a score of 0.713
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The variant is absent from gnomAD v4.1.0 meeting PM2_Supporting.
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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