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.1856C>T (p.Ser619Leu)

CA172110

7285 (ClinVar)

Gene: DNM2
Condition: centronuclear myopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: a90c3958-d390-4f21-907e-aed0899a8a1e
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_001005361.3:c.1856C>T
NM_001005361.3(DNM2):c.1856C>T (p.Ser619Leu)
NC_000019.10:g.10823862C>T
CM000681.2:g.10823862C>T
NC_000019.9:g.10934538C>T
CM000681.1:g.10934538C>T
NC_000019.8:g.10795538C>T
NG_008792.1:g.110784C>T
ENST00000681972.1:n.1287C>T
ENST00000355667.11:c.1856C>T
ENST00000389253.9:c.1856C>T
ENST00000355667.10:c.1856C>T
ENST00000359692.10:c.1844C>T
ENST00000389253.8:c.1856C>T
ENST00000408974.8:c.1844C>T
ENST00000585892.5:c.1856C>T
ENST00000590787.1:n.3355C>T
ENST00000590806.5:n.4044C>T
ENST00000593203.1:n.639C>T
NM_001005360.2:c.1856C>T
NM_001005361.2:c.1856C>T
NM_001005362.2:c.1844C>T
NM_001190716.1:c.1856C>T
NM_004945.3:c.1844C>T
NM_001190716.2:c.1856C>T
NM_001005360.3:c.1856C>T
NM_001005362.3:c.1844C>T
NM_004945.4:c.1844C>T

Pathogenic

Met criteria codes 6
PM2_Supporting PS2 PS4 PS3 PP3 PP2
Not Met criteria codes 1
PM5

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.1856C>T variant in DNM2 is a missense variant predicted to cause substitution of serine by leucine at amino acid 619. This variant is absent from gnomAD v4.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.936, which is above the threshold of 0.7, evidence that correlates with impact to DNM2 function (PP3). DNM2, in which the variant was identified, is defined by the ClinGen CM 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 variant has been reported in at least four probands with centronuclear myopathy that was confirmed by muscle biopsy, one of which was a de novo occurrence with parental relationships confirmed (PMIDs: PMIDs:17932957, 30208955, 34595679, PS4, PS2). In vitro assays demonstrate that the p.S619L variant increases GTPase activity (PMID: 20700106), indicating that this variant impacts protein function. Additionally, a variant-specific zebrafish model (PMID: 23338057) and a variant-specific mouse model (PMID:32809972) recapitulate patient phenotypes of motor problems, early impaired muscle function and force, and myofiber hypotrophy (PS4). 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: PS2, PS4, PM2_Supporting, PP2, PP3. (Congenital Myopathies VCEP specifications version 1; 8/7/2024)
Met criteria codes
PM2_Supporting
The p.Ser619Leu variant is absent from gnomAD v4.1 with adequate coverage.
PS2
The p.S629L variant was identified as de novo with parental relationships confirmed in one individual with severe myopathy.
PS4
The p.Ser619Leu variant has been identified in greater than 4 cases with ptosis, ophthalmoparesis, and muscle biopsy-confirmed centronuclear myopathy. More cases are available in the literature, but PS4 has been maxed out. (PMIDs:17932957, 30208955, 34595679)
PS3
There is a variant-specific zebrafish model (PMID: 23338057) and a variant-specific mouse model (PMID:32809972) that recapitulate patient phenotypes of motor problems, early impaired muscle function and force, and myofiber hypotrophy. Additionally, in vitro assays demonstrate that the p.S619L variant increases GTPase activity (PMID: 20700106), which is a specified assay for the CM VCEP.
PP3
REVEL gives a score of 0.936 which is greater than the CM VCEP cutoff of 0.7.
PP2
DNM2, in which the variant was identified, is defined by the ClinGen CM VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease. (Z=3.48)
Not Met criteria codes
PM5
An additional variant has been identified at this amino acid position, p.Ser619Trp (ClinVar variation ID: 7286). However, the p.Ser619Leu variant has more than enough evidence for pathogenicity and the PM5 code will likely be used for the p.Ser619Trp variant when it is curated by the VCEP.
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