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NM_000130.5(F5):c.5646G>A (p.Trp1882Ter) AND Factor V deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 27, 2018
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:
RCV000778945.4

Allele description [Variation Report for NM_000130.5(F5):c.5646G>A (p.Trp1882Ter)]

NM_000130.5(F5):c.5646G>A (p.Trp1882Ter)

Gene:
F5:coagulation factor V [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q24.2
Genomic location:
Preferred name:
NM_000130.5(F5):c.5646G>A (p.Trp1882Ter)
HGVS:
  • NC_000001.11:g.169525971C>T
  • NG_011806.1:g.65561G>A
  • NM_000130.5:c.5646G>AMANE SELECT
  • NP_000121.2:p.Trp1882Ter
  • NP_000121.2:p.Trp1882Ter
  • LRG_553t1:c.5646G>A
  • LRG_553:g.65561G>A
  • LRG_553p1:p.Trp1882Ter
  • NC_000001.10:g.169495209C>T
  • NM_000130.4:c.5646G>A
Protein change:
W1882*
Links:
dbSNP: rs1557908012
NCBI 1000 Genomes Browser:
rs1557908012
Molecular consequence:
  • NM_000130.5:c.5646G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Factor V deficiency
Synonyms:
Reduced coagulation factor V activity
Identifiers:
MONDO: MONDO:0020586; MedGen: C4317320; Orphanet: 326; Human Phenotype Ontology: HP:0003225

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000915366Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)		Uncertain significance
(Aug 27, 2018) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Clinical and molecular characterization of 6 patients affected by severe deficiency of coagulation factor V: Broadening of the mutational spectrum of factor V gene and in vitro analysis of the newly identified missense mutations.

Montefusco MC, Duga S, Asselta R, Malcovati M, Peyvandi F, Santagostino E, Mannucci PM, Tenchini ML.

Blood. 2003 Nov 1;102(9):3210-6. Epub 2003 Jun 19.

PubMed [citation]
PMID:
12816860

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000915366.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The F5 c.5646G>A (p.Trp1882Ter) variant is a stop-gained variant that is predicted to cause premature truncation of the protein. The p.Trp1882Ter variant is described in one study by Montefusco et al. (2003), in which it is referred to as p.Trp1854Ter and identified in a homozygous state in one individual with a severe bleeding disorder and very significantly reduced factor V levels. Controls data are unavailable for the p.Trp1882Ter variant, which is not found in the 1000 Genomes Project, the Exome Sequencing Project, the Exome Aggregation Consortium, or the Genome Aggregation Database despite being found in a region of good sequencing coverage. It is therefore presumed to be rare. Due to the potential impact of stop-gained variants and the limited supporting evidence, the p.Trp1882Ter variant is classified as a variant of unknown significance but suspicious for pathogenicity for factor V deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 16, 2024