NM_005343.4(HRAS):c.173C>T (p.Thr58Ile) AND Costello syndrome

Germline classification:: Pathogenic (6 submissions)
Last evaluated:: Sep 24, 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:: RCV000013444.36

Allele description [Variation Report for NM_005343.4(HRAS):c.173C>T (p.Thr58Ile)]

NM_005343.4(HRAS):c.173C>T (p.Thr58Ile)

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.173C>T (p.Thr58Ile)

Other names:

NM_176795.4(HRAS):c.173C>T; NM_005343.4(HRAS):c.173C>T

HGVS:

NC_000011.10:g.533883G>A
NG_007666.1:g.6668C>T
NM_001130442.3:c.173C>T
NM_001318054.2:c.-147C>T
NM_005343.4:c.173C>TMANE SELECT
NM_176795.5:c.173C>T
NP_001123914.1:p.Thr58Ile
NP_005334.1:p.Thr58Ile
NP_789765.1:p.Thr58Ile
LRG_506t1:c.173C>T
LRG_506:g.6668C>T
LRG_506p1:p.Thr58Ile
NC_000011.9:g.533883G>A
NM_005343.2:c.173C>T
NM_005343.3:c.173C>T
NM_176795.3:c.173C>T
P01112:p.Thr58Ile
c.173C>T

Protein change:

T58I; THR58ILE

Links:

UniProtKB: P01112#VAR_045978; OMIM: 190020.0011; dbSNP: rs121917758

NCBI 1000 Genomes Browser:

rs121917758

Molecular consequence:

NM_001318054.2:c.-147C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001130442.3:c.173C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005343.4:c.173C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_176795.5:c.173C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000033691	OMIM	no assertion criteria provided	Pathogenic (Mar 15, 2008)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000062127	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Pathogenic (Sep 23, 2014)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18247425, 22488832, 24033266
SCV000188769	Blueprint Genetics	no assertion criteria provided	Pathogenic (Feb 3, 2014)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18247425, 22488832
SCV001587697	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 24, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 18247425, 22488832, 26888048, 28492532
SCV002556564	Genetics and Molecular Pathology, SA Pathology See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 12, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18247425, 22488832, 25741868
SCV002769451	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 2, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 18247425, 22488832, 26888048, 29493581, 31222966, 25741868

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing, literature only

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

See all PubMed Citations (8)

Details of each submission

From OMIM, SCV000033691.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a boy with Costello syndrome (218040), Gripp et al. (2008) identified a heterozygous de novo 173C-T transition in exon 3 of the HRAS gene, resulting in a thr58-to-ile (T58I) substitution in a highly conserved residue in the switch II region of small GTPases. Neither parent carried the mutation, which was present on the paternal allele. At the time of birth, the father and mother were 45 and 34 years old, respectively. The facial features of the patient were less coarse than typical Costello syndrome, but he showed other typical features, including failure to thrive, cognitive impairment, lax skin, deep palmar creases, and pyloric stenosis.

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

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000062127.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (3)

Description

The Thr58Ile variant in HRAS has been reported in three individuals with clinica l features of Costello syndrome (Gripp 2008, Gripp 2012, LMM unpublished data). It was identified to occur de novo in two of these individuals and segregated w ith disease in one affected relative from one of these families. This variant wa s absent from large population studies. Computational prediction tools and conse rvation analysis suggest that this variant may impact the protein, though this i nformation is not predictive enough to determine pathogenicity. In summary, this variant meets our criteria to be classified as pathogenic (http://pcpgm.partner s.org/LMM).

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

From Blueprint Genetics, SCV000188769.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001587697.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 58 of the HRAS protein (p.Thr58Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of Costello syndrome (PMID: 18247425, 22488832, 26888048). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 12610). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is expected to disrupt HRAS function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

#	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

From Genetics and Molecular Pathology, SA Pathology, SCV002556564.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

PS1, PS4_supporting, PM1, PM2, PP5 The HRAS c.173C>T variant is a single nucleotide change from a cytosine to a thymine at position 173 which is predicted to substitute the amino acid threonine at position 58 in the protein to isoleucine. The variant is located in exon 3. This variant has been reported in the literature in patients with Costello syndrome, and this particular variant appears to be associated with an attenuated phenotype and has been described in a father and son (PMID: 22488832; PMID: 18247425) (PS4_supporting). The variant is in dbSNP (rs121917758) but is absent from population databases (PM2). This variant has been classified by the ClinGen RASopathy Variant Curation Expert Panel as Pathogenic and is reported as Pathogenic in the ClinVar database (Variation ID: 12610) (PP5). This variant was detected in both the affected child and her mother.

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

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002769451.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with Costello syndrome (MIM#218040) [PMID: 31222966]. (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity (GeneReviews).(I) 0200 - Variant is predicted to result in a missense amino acid change from threonine to isoleucine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants in the Ras domain (Decipher; PMID 29493581). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as de novo in at least two individuals with Costello syndrome (PMID 18247425; PMID 26888048). It has also been reported in a father and child with an attenuated Costello syndrome phenotype (PMID 22488832). This variant has been classified as pathogenic by the ClinGen RASopathy Variant Curation Expert Panel (ClinVar). (SP) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: May 25, 2025

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