VCV002633786.2 - ClinVar

NM_005343.4(HRAS):c.179_205dup (p.Arg68_Asp69insGlyGlnGluGluTyrSerAlaMetArg)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_005343.4(HRAS):c.179_205dup (p.Arg68_Asp69insGlyGlnGluGluTyrSerAlaMetArg)

Variation ID: 2633786 Accession: VCV002633786.2

Type and length

Duplication, 27 bp

Location

Cytogenetic: 11p15.5 11: 533850-533851 (GRCh38) [ NCBI UCSC ] 11: 533850-533851 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 20, 2023	Oct 8, 2024	May 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_005343.4:c.179_205dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005334.1:p.Arg68_Asp69insGlyGlnGluGluTyrSerAlaMetArg	inframe insertion
NM_176795.5:c.179_205dup MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_789765.1:p.Arg68_Asp69insGlyGlnGluGluTyrSerAlaMetArg	inframe insertion
NM_001130442.3:c.179_205dup	NP_001123914.1:p.Arg68_Asp69insGlyGlnGluGluTyrSerAlaMetArg	inframe insertion
NM_001318054.2:c.-141_-115dup		5 prime UTR
NC_000011.10:g.533852_533878dup
NC_000011.9:g.533852_533878dup
NG_007666.1:g.6674_6700dup
NG_121454.1:g.161_187dup
NG_121454.2:g.161_187dup
LRG_506:g.6674_6700dup
LRG_506t1:c.179_205dup	LRG_506p1:p.Arg68_Asp69insGlyGlnGluGluTyrSerAlaMetArg

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000011.10:533850:CCCGCATGGCGCTGTACTCCTCCTGGCC:CCCGCATGGCGCTGTACTCCTCCTGGCCCCGCATGGCGCTGTACTCCTCCTGGCC

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
HRAS		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	12	723
LRRC56		-	-	GRCh38 GRCh38 GRCh37	346	1057

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
HRAS-related disorder	Likely pathogenic (1)	no assertion criteria provided	May 20, 2024	RCV003400256.5

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (May 20, 2024)	no assertion criteria provided Method: clinical testing	HRAS-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004103212.2 First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024	Comment: The HRAS c.179_205dup27 variant is predicted to result in an in-frame duplication (p.Gly60_Arg68dup). To our knowledge, this variant has not been reported in the literature … (more) The HRAS c.179_205dup27 variant is predicted to result in an in-frame duplication (p.Gly60_Arg68dup). To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. Of note, this variant has been reported de novo at PreventionGenetics in a fetal demise with features suspect of Noonan syndrome, including cystic hygroma, pleural effusion, pelviectasis, and possibly congenital heart disease (Internal Data). Similar inframe duplications (p.Glu62_Arg68dup, p.Glu63_Asp69dup) have been reported in individuals with Costello syndrome with functional studies supporting their pathogenicity (Nagai et al. 2022. PubMed ID: 34618388). Additionally, this duplication overlaps multiple pathogenic missense variants (p.Gly60Asp, p.Gly60Val, p.Glu63Lys) reported in individuals with HRAS-related disease (Gripp et al. 2015. PubMed ID: 25914166; Gripp et al. 2017. PubMed ID: 28139825; van der Burgt et al. 2007. PubMed ID: 17412879). Taken together, this variant is interpreted as likely pathogenic. (less)

Comment:

The HRAS c.179_205dup27 variant is predicted to result in an in-frame duplication (p.Gly60_Arg68dup). To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. Of note, this variant has been reported de novo at PreventionGenetics in a fetal demise with features suspect of Noonan syndrome, including cystic hygroma, pleural effusion, pelviectasis, and possibly congenital heart disease (Internal Data). Similar inframe duplications (p.Glu62_Arg68dup, p.Glu63_Asp69dup) have been reported in individuals with Costello syndrome with functional studies supporting their pathogenicity (Nagai et al. 2022. PubMed ID: 34618388). Additionally, this duplication overlaps multiple pathogenic missense variants (p.Gly60Asp, p.Gly60Val, p.Glu63Lys) reported in individuals with HRAS-related disease (Gripp et al. 2015. PubMed ID: 25914166; Gripp et al. 2017. PubMed ID: 28139825; van der Burgt et al. 2007. PubMed ID: 17412879). Taken together, this variant is interpreted as likely pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Oct 13, 2024

ClinVar Genomic variation as it relates to human health

NM_005343.4(HRAS):c.179_205dup (p.Arg68_Asp69insGlyGlnGluGluTyrSerAlaMetArg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...