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 label mismatch: PPP1CB vs undefined
  • 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_002709.3(PPP1CB):c.548A>T (p.Glu183Val)

CA10586684

254651 (ClinVar)

Gene: PPP1CB
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 6c3edeaa-962b-45a3-9495-40aee0832601
Approved on: 2024-12-03
Published on: 2025-03-25

HGVS expressions

NM_002709.3:c.548A>T
NM_002709.3(PPP1CB):c.548A>T (p.Glu183Val)
NC_000002.12:g.28783934A>T
CM000664.2:g.28783934A>T
NC_000002.11:g.29006800A>T
CM000664.1:g.29006800A>T
NC_000002.10:g.28860304A>T
NG_052878.1:g.37187A>T
ENST00000420282.6:c.548A>T
ENST00000427786.2:c.*508A>T
ENST00000441461.6:c.548A>T
ENST00000455580.6:c.464A>T
ENST00000703171.1:c.*595A>T
ENST00000703172.1:c.464A>T
ENST00000703173.1:c.548A>T
ENST00000703174.1:c.671A>T
ENST00000703176.1:c.515A>T
ENST00000703177.1:c.*508A>T
ENST00000703183.1:n.431A>T
ENST00000395366.3:c.548A>T
ENST00000296122.10:c.548A>T
ENST00000358506.6:c.548A>T
ENST00000395366.2:c.548A>T
ENST00000455580.5:c.464A>T
ENST00000462832.5:n.375A>T
NM_002709.2:c.548A>T
NM_206876.1:c.548A>T
NM_206876.2:c.548A>T
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Pathogenic

Met criteria codes 5
PS2 PS4_Supporting PP2 PM2_Supporting PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PPP1CB Version 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.548A>T (p.Glu183Val) variant in PPP1CB is a missense variant predicted to cause substitution of glutamate by valine at amino acid 183. This variant is absent from gnomAD v2 (PM2_Supporting). PPP1CB, in which the variant was identified, is defined by the ClinGen RASopathy 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 missense Z-score is 4.33 which is above the threshold set by the Rasopathy VCEP (PP2). This variant was observed in a proband with a phenotype consistent with RASopathy (PS4_Supporting; PMID:27681385). This variant has also been identified as a de novo occurrence with confirmed parental relationships in 1 individual with features of RASopathy (PS2; PMID:27681385). The variant occurs at the same amino acid residue as the PPP1CB c.548A>C (p.Glu183Ala) variant, which has been classified as pathogenic by the ClinGen RASOpathy VCEP (PM5). Based on ACMG/AMP criteria, this variant has enough supporting evidence to be classified as likely pathogenic; however, the RASopathy VCEP has upgraded this classification to pathogenic based on ClinGen policy due to the strength of evidence for the PM5 code. In summary, this variant currently meets the criteria to be classified as pathogenic for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: PS2, PM5, PP2, PS4_Supporting, PM2_Supporting. (RASopathy VCEP specifications version 1.3; 12/3/2024)
Met criteria codes
PS2
This variant has been identified as a de novo occurrence with confirmed parental relationships in 1 individual with features of RASopathy (PMID: 27681385)
PS4_Supporting
This variant has been reported in 1 proband with features of RASopathy (PMID:27681385)
PP2
PPP1CB, in which the variant was identified, is defined by the ClinGen RASopathy 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 missense Z-score is 4.33 which is above the threshold set by the Rasopathy VCEP.
PM2_Supporting
This variant is absent from gnomAD v4
PM5
Glu183Ala has been determined to be pathogenic by the ClinGen RASopathy VCEP
Curation History
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