NM_005343.4(HRAS):c.484G>A (p.Glu162Lys) AND Costello syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 2, 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:: RCV001337613.7

Allele description [Variation Report for NM_005343.4(HRAS):c.484G>A (p.Glu162Lys)]

NM_005343.4(HRAS):c.484G>A (p.Glu162Lys)

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.484G>A (p.Glu162Lys)

HGVS:

NC_000011.10:g.532722C>T
NG_007666.1:g.7829G>A
NM_001130442.3:c.484G>A
NM_001318054.2:c.247G>A
NM_005343.4:c.484G>AMANE SELECT
NM_176795.5:c.*53G>A
NP_001123914.1:p.Glu162Lys
NP_001304983.1:p.Glu83Lys
NP_005334.1:p.Glu162Lys
LRG_506t1:c.484G>A
LRG_506:g.7829G>A
LRG_506p1:p.Glu162Lys
NC_000011.9:g.532722C>T
NM_005343.2:c.484G>A

Protein change:

E162K

Links:

dbSNP: rs1564787942

NCBI 1000 Genomes Browser:

rs1564787942

Molecular consequence:

NM_176795.5:c.*53G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001130442.3:c.484G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318054.2:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005343.4:c.484G>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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Homologene neighbors for GEO Profiles (Select 125819229) (0)
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Gene Links for GEO Profiles (Select 125826926) (1)
Gene
OR10D1P olfactory receptor family 10 subfamily D member 1 pseudogene [Homo sapie...
OR10D1P olfactory receptor family 10 subfamily D member 1 pseudogene [Homo sapiens]
Gene ID:26541

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001531220	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 2, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001531220

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 2, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001531220.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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 not expected to disrupt HRAS protein function. ClinVar contains an entry for this variant (Variation ID: 1034833). 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 glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 162 of the HRAS protein (p.Glu162Lys).

#	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

Last Updated: Sep 29, 2024

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