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NM_002072.5(GNAQ):c.548G>A (p.Arg183Gln) AND Capillary malformation

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Oct 14, 2023
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:
RCV000043593.8

Allele description [Variation Report for NM_002072.5(GNAQ):c.548G>A (p.Arg183Gln)]

NM_002072.5(GNAQ):c.548G>A (p.Arg183Gln)

Gene:
GNAQ:G protein subunit alpha q [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q21.2
Genomic location:
Preferred name:
NM_002072.5(GNAQ):c.548G>A (p.Arg183Gln)
HGVS:
  • NC_000009.12:g.77797577C>T
  • NG_027904.2:g.238727G>A
  • NM_002072.5:c.548G>AMANE SELECT
  • NP_002063.2:p.Arg183Gln
  • LRG_1110t1:c.548G>A
  • LRG_1110:g.238727G>A
  • LRG_1110p1:p.Arg183Gln
  • NC_000009.11:g.80412493C>T
  • NM_002072.2:c.548G>A
  • NM_002072.4:c.548G>A
  • P50148:p.Arg183Gln
  • p.R183Q
Protein change:
R183Q; ARG183GLN
Links:
UniProtKB: P50148#VAR_067270; OMIM: 600998.0001; dbSNP: rs397514698
NCBI 1000 Genomes Browser:
rs397514698
Molecular consequence:
  • NM_002072.5:c.548G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Capillary malformation (CMC)
Synonyms:
CAPILLARY MALFORMATIONS; Capillary malformations, congenital
Identifiers:
MONDO: MONDO:0016231; MedGen: C0340803; Human Phenotype Ontology: HP:0025104

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000071611OMIM
no assertion criteria provided
Pathogenic
(Dec 1, 2014)
somaticliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV004176929Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 14, 2023)
somaticclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedsomaticyesnot providednot providednot providednot providednot providedclinical testing
not providedsomaticnot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Sturge-Weber syndrome and port-wine stains caused by somatic mutation in GNAQ.

Shirley MD, Tang H, Gallione CJ, Baugher JD, Frelin LP, Cohen B, North PE, Marchuk DA, Comi AM, Pevsner J.

N Engl J Med. 2013 May 23;368(21):1971-9. doi: 10.1056/NEJMoa1213507. Epub 2013 May 8.

PubMed [citation]
PMID:
23656586
PMCID:
PMC3749068

Novel genetic mutations in a sporadic port-wine stain.

Lian CG, Sholl LM, Zakka LR, O TM, Liu C, Xu S, Stanek E, Garcia E, Jia Y, MacConaill LE, Murphy GF, Waner M, Mihm MC Jr.

JAMA Dermatol. 2014 Dec;150(12):1336-40.

PubMed [citation]
PMID:
25188413
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000071611.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Shirley et al. (2013) performed whole-genome sequencing of DNA from paired samples of visibly affected and normal tissue from 3 patients with Sturge-Weber syndrome (SWS; 185300) and identified 1 nonsynonymous somatic single-nucleotide variant, a c.548G-A transition in the GNAQ gene, resulting in an arg183-to-gln (R183Q) substitution at a highly conserved residue, that was present in all 3 affected samples and was not present in the normal-appearing samples. Screening of additional SWS patients as well as individuals with nonsyndromic port-wine stains (163000) revealed that all 9 SWS patients were positive for the R183Q mutation in port-wine-stained skin, 6 (86%) of 7 participants with SWS were negative for the mutation in visibly normal skin, and 12 (92%) of 13 participants with nonsyndromic port-wine stains were positive for the mutation. The mutation was also detected in brain samples from 15 (83%) of 18 SWS patients, whereas all 6 brain samples from normal controls were negative. Transfection studies in HEK 293T cells showed significant activation of ERK (600997) by the R183Q mutant compared to control. Overall, 23 (88%) of 26 SWS patients were positive for the gain-of-function R183Q mutation in either port wine-stained skin or brain tissue. Shirley et al. (2013) suggested that nonsyndromic port-wine stains may represent a late origin of the somatic GNAQ mutation in vascular endothelial cells, whereas in Sturge-Weber syndrome, the mutation may occur earlier in development, in progenitor cells that are precursors to a larger variety of cell types and tissues, leading to the syndromic phenotype. Five (0.7%) of 669 samples from the 1000 Genomes Project database were positive for R183Q; noting that the reported prevalence of port-wine stains is 0.3% to 0.5%, Shirley et al. (2013) hypothesized that the 0.7% prevalence in that database represented the occurrence of port-wine stains in the population.

In tissue from a patient with a sporadic long-standing unilateral facial port-wine stain, Lian et al. (2014) detected the GNAQ R183Q mutation at an allelic fraction of 0.05 in PWS tissue; the mutation was not found in paired normal tissue. The percentage of GNAQ mutation was consistent with the percentage of lesional endothelial cells in the specimen.

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

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV004176929.1

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

Description

A GNAQ c.548G>A (p.Arg183Gln) variant was identified at an allelic fraction consistent with somatic origin. This variant has been reported in multiple individuals affected with Sturge-Weber syndrome, nonsyndromic port-wine stains, and phakomatosis pigmentovascularis with capillary malformation and hemihypertrophy (Shirley MD et al., PMID: 23656586; Nakashima M et al., PMID: 25374402; Frigerio A et al., PMID: 26192947; Thomas AC et al., PMID: 26778290; He R et al., PMID: 32613723). This variant has been reported in the ClinVar database as a pathogenic/likely pathogenic variant by multiple submitters (ClinVar ID: 50853), and it has been reported in multiple cases in the cancer database COSMIC (Genomic ID: COSV54106047). This variant is absent from the general population (gnomAD v.3.1.2), indicating it is not a common variant. This variant resides within the GTP-binding site of the G2 motif, which is defined as a critical functional domain (Nakashima M et al., PMID: 25374402). Computational predictors indicate that the GNAQ c.548G>A (p.Arg183Gln) variant is damaging, evidence that correlates with impact on GNAQ function. In support of this prediction, functional studies show that this variant increases activation of the mitogen-activated protein kinase (MAPK) pathway and increases angiopoietin-2 expression (Shirley MD et al., PMID: 23656586; Huang L et al., PMID: 34670408). GNAQ is a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease. Based on an internally-developed protocol informed by the ACMG/AMP guidelines (Richards S et al., PMID: 25741868), the GNAQ c.548G>A (p.Arg183Gln) variant is classified as pathogenic.

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

Last Updated: Aug 11, 2024