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.1564C>T (p.Arg522Cys)

CA404039368

986927 (ClinVar)

Gene: DNM2 (HGNC:1785)
Condition: centronuclear myopathy (MONDO:0018947)
Inheritance Mode: Autosomal dominant inheritance
UUID: 2422e9c5-0079-408f-87b1-69444c139744
Approved on: 2025-09-08
Published on: 2025-09-19

HGVS expressions

NM_001005361.3(DNM2):c.1564C>T (p.Arg522Cys)
NM_001005361.3:c.1564C>T
NC_000019.10:g.10812270C>T
CM000681.2:g.10812270C>T
NC_000019.9:g.10922946C>T
CM000681.1:g.10922946C>T
NC_000019.8:g.10783946C>T
NG_008792.1:g.99192C>T
ENST00000681972.1:n.995C>T
ENST00000355667.11:c.1564C>T
ENST00000389253.9:c.1564C>T
ENST00000355667.10:c.1564C>T
ENST00000359692.10:c.1552C>T
ENST00000389253.8:c.1564C>T
ENST00000408974.8:c.1552C>T
ENST00000585892.5:c.1564C>T
ENST00000587830.2:c.838C>T
ENST00000590787.1:n.3063C>T
ENST00000590806.5:n.3752C>T
NM_001005360.2:c.1564C>T
NM_001005361.2:c.1564C>T
NM_001005362.2:c.1552C>T
NM_001190716.1:c.1564C>T
NM_004945.3:c.1552C>T
NM_001190716.2:c.1564C>T
NM_001005360.3:c.1564C>T
NM_001005362.3:c.1552C>T
NM_004945.4:c.1552C>T
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PP2 PM5 PS4_Supporting
Not Met criteria codes 3
BS1 BP4 BA1

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 variant NM_001005361.3:c.1564C>T in DNM2 is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 522 (p.Arg522Cys). The highest population minor allele frequency in gnomAD v4.1.0 is 8.526e-7 (1/1172834 alleles) in non-Finnish European which meets 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 REVEL computational prediction analysis tool produced a score of 0.746, which is above the threshold of 0.7, evidence that correlates with impact to DNM2 function (PP3). Two different missense variants, p.Arg522His and p.Arg522Leu (ClinVar IDs: 158514 and 373110), in the same codon have been classified as (likely) pathogenic on ClinVar, of which p.Arg522His has been classified as pathogenic for centronuclear myopathy by the ClinGen Congenital Myopathies VCEP (PM5). This variant has been reported in one proband with centronuclear myopathy who presented with predominantly distal muscle weakness, ptosis, ophthalmoplegia/ paresis, facial weakness, weak deep tendon reflexes, stepping gait, central nuclei, fiber hypotrophy, and Type 1 fiber predominance (0.25pts, PS4_Supporting; PMID: 22396310). In summary, the variant meets criteria to be classified as likely pathogenic for centronuclear myopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PM5, PS4_Supporting, PM2_Supporting, PP2, PP3 (ClinGen Congenital Myopathies VCEP specifications version 1.0.0; September 8th, 2025).
Met criteria codes
PM2_Supporting
The MAF in gnomAD v.4.1.0 is 8.526e-7 (1/1172834) in non-Finnish European which meets PM2_Supporting
PP3
The REVEL computational prediction analysis tool produced a score of 0.746, which is above the threshold of 0.7
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
PM5
Two different missense variants, p.Arg522His and p.Arg522Leu (ClinVar IDs: 158514 and 373110), in the same codon have been classified as (likely) pathogenic on ClinVar, of which p.Arg522His has been classified as pathogenic for centronuclear myopathy by the ClinGen Congenital Myopathies VCEP
PS4_Supporting
One proband with centronuclear myopathy presented with predominantly distal muscle weakness, ptosis, ophthalmoplegia/paresis, facial weakness, weak deep tendon reflexes, stepping gait, central nuclei, fiber hypotrophy, and Type 1 fiber predominance (0.25pts; PMID: 22396310).
Not Met criteria codes
BS1
The MAF in gnomAD v.4.1.0 is 8.526e-7 (1/1172834) in non-Finnish European which meets PM2_Supporting
BP4
The REVEL computational prediction analysis tool produced a score of 0.746, which meets PP3
BA1
The MAF in gnomAD v.4.1.0 is 8.526e-7 (1/1172834) in non-Finnish European which meets PM2_Supporting
Curation History
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