VCV001731751.4 - ClinVar

NM_005633.4(SOS1):c.3472C>T (p.Arg1158Ter)

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.

(3)

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.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_005633.4(SOS1):c.3472C>T (p.Arg1158Ter)

Variation ID: 1731751 Accession: VCV001731751.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 2p22.1 2: 38987511 (GRCh38) [ NCBI UCSC ] 2: 39214652 (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 29, 2022	May 1, 2024	Aug 16, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_005633.4:c.3472C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005624.2:p.Arg1158Ter	nonsense
NM_001382394.1:c.3451C>T	NP_001369323.1:p.Arg1151Ter	nonsense
NM_001382395.1:c.3427C>T	NP_001369324.1:p.Arg1143Ter	nonsense
NC_000002.12:g.38987511G>A
NC_000002.11:g.39214652G>A
NG_007530.1:g.137953C>T
LRG_754:g.137953C>T
LRG_754t1:c.3472C>T	LRG_754p1:p.Arg1158Ter

... more HGVS ... less HGVS

Protein change

R1158*, R1151*, R1143*

Other names

Canonical SPDI

NC_000002.12:38987510:G:A

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.
SOS1		No evidence available	No evidence available	GRCh38 GRCh37	1661	1764

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.
not provided	Uncertain significance (1)	criteria provided, single submitter	Jun 22, 2023	RCV003236925.1
RASopathy	Uncertain significance (1)	criteria provided, single submitter	Aug 16, 2023	RCV003775636.2
Cardiovascular phenotype	Uncertain significance (1)	criteria provided, single submitter	Dec 14, 2021	RCV002457297.2

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.
Uncertain significance (Jun 22, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV003935627.1 First in ClinVar: Jul 01, 2023 Last updated: Jul 01, 2023	Comment: Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation as the last 176 amino acids are … (more) Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation as the last 176 amino acids are lost, although loss-of-function variants have not been reported downstream of this position in the protein; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 29493581) (less)
Uncertain significance (Aug 16, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	RASopathy Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004642744.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Comment: This sequence change creates a premature translational stop signal (p.Arg1158) in the SOS1 gene. While this is not anticipated to result in nonsense mediated decay, … (more) This sequence change creates a premature translational stop signal (p.Arg1158) in the SOS1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 176 amino acid(s) of the SOS1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SOS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1731751). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. (less)
Uncertain significance (Dec 14, 2021)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Cardiovascular phenotype Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV002613943.2 First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024	Comment: The p.R1158* variant (also known as c.3472C>T), located in coding exon 22 of the SOS1 gene, results from a C to T substitution at nucleotide … (more) The p.R1158* variant (also known as c.3472C>T), located in coding exon 22 of the SOS1 gene, results from a C to T substitution at nucleotide position 3472. This changes the amino acid from an arginine to a stop codon within coding exon 22. This alteration occurs at the 3' terminus of theSOS1 gene, is not expected to trigger nonsense-mediated mRNAdecay, and impacts the last 176 amino acids of the protein. The exact functional effect of this alteration is unknown. Additionally, loss of function of SOS1 has not been clearly established as a mechanism of disease. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)

Comment:

Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation as the last 176 amino acids are lost, although loss-of-function variants have not been reported downstream of this position in the protein; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 29493581)

Comment:

This sequence change creates a premature translational stop signal (p.Arg1158*) in the SOS1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 176 amino acid(s) of the SOS1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SOS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1731751). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

Comment:

The p.R1158* variant (also known as c.3472C>T), located in coding exon 22 of the SOS1 gene, results from a C to T substitution at nucleotide position 3472. This changes the amino acid from an arginine to a stop codon within coding exon 22. This alteration occurs at the 3' terminus of theSOS1 gene, is not expected to trigger nonsense-mediated mRNAdecay, and impacts the last 176 amino acids of the protein. The exact functional effect of this alteration is unknown. Additionally, loss of function of SOS1 has not been clearly established as a mechanism of disease. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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 Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_005633.4(SOS1):c.3472C>T (p.Arg1158Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...