NM_002709.3(PPP1CB):c.201A>G (p.Gln67=) AND RASopathy

Germline classification:: Benign (1 submission)
Last evaluated:: Dec 3, 2024
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV005253651.1

Allele description [Variation Report for NM_002709.3(PPP1CB):c.201A>G (p.Gln67=)]

NM_002709.3(PPP1CB):c.201A>G (p.Gln67=)

Gene:

PPP1CB:protein phosphatase 1 catalytic subunit beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.2

Genomic location:

Preferred name:

NM_002709.3(PPP1CB):c.201A>G (p.Gln67=)

Other names:

NM_002709.3(PPP1CB):c.201A>G; p.Gln67=

HGVS:

NC_000002.12:g.28778825A>G
NG_052878.1:g.32078A>G
NM_002709.3:c.201A>GMANE SELECT
NM_206876.2:c.201A>G
NP_002700.1:p.Gln67=
NP_996759.1:p.Gln67=
NP_996759.1:p.Gln67=
NC_000002.11:g.29001691A>G
NM_002709.2:c.201A>G
NM_206876.1:c.201A>G
p.Gln67Gln

Links:

dbSNP: rs1128416

Molecular consequence:

NM_002709.3:c.201A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_206876.2:c.201A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: RASopathy
Synonyms:: rasopathies; Noonan spectrum disorder
Identifiers:: MONDO: MONDO:0021060; MedGen: C5555857

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005903439	ClinGen RASopathy Variant Curation Expert Panel	reviewed by expert panel (ClinGen RASopathy ACMG Specifications PPP1CB V1.3.0)	Benign (Dec 3, 2024)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005903439

ClinGen RASopathy Variant Curation Expert Panel

reviewed by expert panel

(ClinGen RASopathy ACMG Specifications PPP1CB V1.3.0)

Benign
(Dec 3, 2024)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Details of each submission

From ClinGen RASopathy Variant Curation Expert Panel, SCV005903439.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

The c.201A>G (p.Gln67=) variant in PPP1CB is a synonymous (silent) variant that is not predicted by SpliceAI to impact splicing. In addition, the computational predictor REVEL does not predict a damaging effect on PPP1CB function (BP4, BP7). The filtering allele frequency in gnomAD v2 is 60.64% in the European (non-Finnish) population, which is higher than the ClinGen RASopathy VCEP threshold (>0.0005) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as benign for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: BA1, BP4, BP7. (RASopathy VCEP specifications version 1.3; 12/3/2024)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 1, 2026

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