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NM_007144.3(PCGF2):c.194C>T (p.Pro65Leu) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 28, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002536572.3

Allele description [Variation Report for NM_007144.3(PCGF2):c.194C>T (p.Pro65Leu)]

NM_007144.3(PCGF2):c.194C>T (p.Pro65Leu)

Gene:
PCGF2:polycomb group ring finger 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q12
Genomic location:
Preferred name:
NM_007144.3(PCGF2):c.194C>T (p.Pro65Leu)
HGVS:
  • NC_000017.11:g.38739601G>A
  • NM_001369614.1:c.194C>T
  • NM_001369615.1:c.194C>T
  • NM_007144.3:c.194C>TMANE SELECT
  • NP_001356543.1:p.Pro65Leu
  • NP_001356544.1:p.Pro65Leu
  • NP_009075.1:p.Pro65Leu
  • NC_000017.10:g.36895854G>A
  • NM_007144.2:c.194C>T
Protein change:
P65L; PRO65LEU
Links:
OMIM: 600346.0001
Molecular consequence:
  • NM_001369614.1:c.194C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369615.1:c.194C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007144.3:c.194C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003563757Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Oct 28, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Missense Mutations of the Pro65 Residue of PCGF2 Cause a Recognizable Syndrome Associated with Craniofacial, Neurological, Cardiovascular, and Skeletal Features.

Turnpenny PD, Wright MJ, Sloman M, Caswell R, van Essen AJ, Gerkes E, Pfundt R, White SM, Shaul-Lotan N, Carpenter L, Schaefer GB, Fryer A, Innes AM, Forbes KP, Chung WK, McLaughlin H, Henderson LB, Roberts AE, Heath KE, Paumard-Hernández B, Gener B; DDD study., et al.

Am J Hum Genet. 2018 Nov 1;103(5):786-793. doi: 10.1016/j.ajhg.2018.09.012. Epub 2018 Oct 18. Erratum in: Am J Hum Genet. 2018 Dec 6;103(6):1054-1055. doi: 10.1016/j.ajhg.2018.11.009.

PubMed [citation]
PMID:
30343942
PMCID:
PMC6218713

Details of each submission

From Ambry Genetics, SCV003563757.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.194C>T (p.P65L) alteration is located in exon 4 (coding exon 2) of the PCGF2 gene. This alteration results from a C to T substitution at nucleotide position 194, causing the proline (P) at amino acid position 65 to be replaced by a leucine (L). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been identified as a recurrent de novo variant in multiple individuals with Turnpenny-Fry syndrome with features including a recognizable facial gestalt, intellectual disability, feeding problems, impaired growth, and a range of brain, cardiovascular, and skeletal abnormalities (Turnpenny, 2018; Ambry internal data). In one family, this variant was detected as mosaic in the asymptomatic mother (Turnpenny, 2018). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 29, 2024