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NM_005343.4(HRAS):c.178G>A (p.Gly60Ser) AND Costello syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 29, 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:
RCV000818197.6

Allele description [Variation Report for NM_005343.4(HRAS):c.178G>A (p.Gly60Ser)]

NM_005343.4(HRAS):c.178G>A (p.Gly60Ser)

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.178G>A (p.Gly60Ser)
HGVS:
  • NC_000011.10:g.533878C>T
  • NG_007666.1:g.6673G>A
  • NM_001130442.3:c.178G>A
  • NM_001318054.2:c.-142G>A
  • NM_005343.4:c.178G>AMANE SELECT
  • NM_176795.5:c.178G>A
  • NP_001123914.1:p.Gly60Ser
  • NP_005334.1:p.Gly60Ser
  • NP_789765.1:p.Gly60Ser
  • LRG_506t1:c.178G>A
  • LRG_506:g.6673G>A
  • LRG_506p1:p.Gly60Ser
  • NC_000011.9:g.533878C>T
  • NM_005343.2:c.178G>A
Protein change:
G60S
Links:
dbSNP: rs1589792804
NCBI 1000 Genomes Browser:
rs1589792804
Molecular consequence:
  • NM_001318054.2:c.-142G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001130442.3:c.178G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005343.4:c.178G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_176795.5:c.178G>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
SCV000958797Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Nov 29, 2022)
germlineclinical testing

PubMed (3)
[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

An attenuated phenotype of Costello syndrome in three unrelated individuals with a HRAS c.179G>A (p.Gly60Asp) mutation correlates with uncommon functional consequences.

Gripp KW, Sol-Church K, Smpokou P, Graham GE, Stevenson DA, Hanson H, Viskochil DH, Baker LC, Russo B, Gardner N, Stabley DL, Kolbe V, Rosenberger G.

Am J Med Genet A. 2015 Sep;167A(9):2085-97. doi: 10.1002/ajmg.a.37128. Epub 2015 Apr 25.

PubMed [citation]
PMID:
25914166
PMCID:
PMC4830354

Attenuated phenotype of Costello syndrome and early death in a patient with an HRAS mutation (c.179G>T; p.Gly60Val) affecting signalling dynamics.

Gripp KW, Kolbe V, Brandenstein LI, Rosenberger G.

Clin Genet. 2017 Sep;92(3):332-337. doi: 10.1111/cge.12980. Epub 2017 Mar 30.

PubMed [citation]
PMID:
28139825
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000958797.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

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.Gly60 amino acid residue in HRAS. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 25914166, 28139825). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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: 660897). 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 60 of the HRAS protein (p.Gly60Ser).

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

Last Updated: Feb 20, 2024