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NM_005343.4(HRAS):c.37G>A (p.Gly13Ser) AND Costello syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 18, 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:
RCV002524694.4

Allele description [Variation Report for NM_005343.4(HRAS):c.37G>A (p.Gly13Ser)]

NM_005343.4(HRAS):c.37G>A (p.Gly13Ser)

Genes:
HRAS:HRas proto-oncogene, GTPase [Gene - OMIM - HGNC]
LRRC56:leucine rich repeat containing 56 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.5
Genomic location:
Preferred name:
NM_005343.4(HRAS):c.37G>A (p.Gly13Ser)
HGVS:
  • NC_000011.10:g.534286C>T
  • NG_007666.1:g.6265G>A
  • NM_001130442.3:c.37G>A
  • NM_001318054.2:c.-283G>A
  • NM_005343.4:c.37G>AMANE SELECT
  • NM_176795.5:c.37G>A
  • NP_001123914.1:p.Gly13Ser
  • NP_005334.1:p.Gly13Ser
  • NP_789765.1:p.Gly13Ser
  • NP_789765.1:p.Gly13Ser
  • LRG_506t1:c.37G>A
  • LRG_506:g.6265G>A
  • LRG_506p1:p.Gly13Ser
  • NC_000011.9:g.534286C>T
  • NM_176795.4:c.37G>A
Protein change:
G13S
Links:
dbSNP: rs104894228
NCBI 1000 Genomes Browser:
rs104894228
Molecular consequence:
  • NM_001318054.2:c.-283G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001130442.3:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005343.4:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_176795.5:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Costello syndrome (CSTLO)
Synonyms:
FACIOCUTANEOSKELETAL SYNDROME; FCS SYNDROME
Identifiers:
MONDO: MONDO:0009026; MedGen: C0587248; Orphanet: 3071; OMIM: 218040

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003292872Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(May 18, 2022)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

HRAS mutation analysis in Costello syndrome: genotype and phenotype correlation.

Gripp KW, Lin AE, Stabley DL, Nicholson L, Scott CI Jr, Doyle D, Aoki Y, Matsubara Y, Zackai EH, Lapunzina P, Gonzalez-Meneses A, Holbrook J, Agresta CA, Gonzalez IL, Sol-Church K.

Am J Med Genet A. 2006 Jan 1;140(1):1-7.

PubMed [citation]
PMID:
16329078

HRAS mutations in Costello syndrome: detection of constitutional activating mutations in codon 12 and 13 and loss of wild-type allele in malignancy.

Estep AL, Tidyman WE, Teitell MA, Cotter PD, Rauen KA.

Am J Med Genet A. 2006 Jan 1;140(1):8-16.

PubMed [citation]
PMID:
16372351
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003292872.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Gly13 amino acid residue in HRAS. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16329078, 16372351, 18042262, 21438134). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects HRAS function (PMID: 24224811). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt HRAS protein function. ClinVar contains an entry for this variant (Variation ID: 376323). This variant has not been reported in the literature in individuals affected with HRAS-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 13 of the HRAS protein (p.Gly13Ser).

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

Last Updated: Feb 25, 2025