VCV000916698.4 - ClinVar

NM_001114753.3(ENG):c.774C>G (p.Tyr258Ter)

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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001114753.3(ENG):c.774C>G (p.Tyr258Ter)

Variation ID: 916698 Accession: VCV000916698.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9q34.11 9: 127825273 (GRCh38) [ NCBI UCSC ] 9: 130587552 (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	Jun 13, 2020	Jun 13, 2020	Sep 10, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NM_001114753.3:c.774C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001108225.1:p.Tyr258Ter	nonsense
NM_000118.4:c.774C>G	NP_000109.1:p.Tyr258Ter	nonsense
NM_001278138.2:c.228C>G	NP_001265067.1:p.Tyr76Ter	nonsense
NM_001406715.1:c.774C>G	NP_001393644.1:p.Tyr258Ter	nonsense
NC_000009.12:g.127825273G>C
NC_000009.11:g.130587552G>C
NG_009551.1:g.34496C>G
LRG_589:g.34496C>G
LRG_589t1:c.774C>G	LRG_589p1:p.Tyr258Ter
LRG_589t2:c.774C>G	LRG_589p2:p.Tyr258Ter

... more HGVS ... less HGVS

Protein change

Y258*, Y76*

Other names

Canonical SPDI

NC_000009.12:127825272:G:C

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

loss_of_function_variant; Sequence Ontology [ SO:0002054]

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.

0.00040 (A)

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

Links

dbSNP: rs537154767 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.
ENG		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1101	1612

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.
Telangiectasia, hereditary hemorrhagic, type 1	Pathogenic (1)	criteria provided, single submitter	Sep 10, 2019	RCV001172494.4

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.
Pathogenic (Sep 10, 2019)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Telangiectasia, hereditary hemorrhagic, type 1 (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	Breda Genetics srl Accession: SCV001250895.1 First in ClinVar: Jun 13, 2020 Last updated: Jun 13, 2020	Comment: The variant c.774C>G (p.Tyr258) creates a premature stop codon at amino acid position Tyr258 which is likely to result in a truncated protein or protein … (more) The variant c.774C>G (p.Tyr258) creates a premature stop codon at amino acid position Tyr258 which is likely to result in a truncated protein or protein loss due to nonsense-mediated messenger decay (NMD). This variant has not been reported in dbSNP, gnomAD, 1000 Genomes, NHLI Exome Sequencing Project (ESP) or ClinVar. The variant c.774C>G (p.Tyr258*) is reported as pathogenic in the HHT Mutation Database (ENG), with 6 other pathogenic mutations (nonsense, frameshift) that fall on the same amminoacid position. Current data suggest that approximately two thirds of variants in the ENG gene are functionally null alleles (McDonald et al., 2000, PMID: 20301525). (less)

Comment:

The variant c.774C>G (p.Tyr258*) creates a premature stop codon at amino acid position Tyr258 which is likely to result in a truncated protein or protein loss due to nonsense-mediated messenger decay (NMD). This variant has not been reported in dbSNP, gnomAD, 1000 Genomes, NHLI Exome Sequencing Project (ESP) or ClinVar. The variant c.774C>G (p.Tyr258*) is reported as pathogenic in the HHT Mutation Database (ENG), with 6 other pathogenic mutations (nonsense, frameshift) that fall on the same amminoacid position. Current data suggest that approximately two thirds of variants in the ENG gene are functionally null alleles (McDonald et al., 2000, PMID: 20301525).

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
loss_of_function_variant (SO:0002054)			Breda Genetics srl Accession: SCV001250895.1

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 rs537154767 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 06, 2023

ClinVar Genomic variation as it relates to human health

NM_001114753.3(ENG):c.774C>G (p.Tyr258Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs537154767 ...