NM_000130.4(F5):c.1601G>A (p.Arg534Gln) AND Factor V deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 6, 2015
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:: RCV000205002.1

Allele description

NM_000130.4(F5):c.1601G>A (p.Arg534Gln)

Gene:

F5:coagulation factor V [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q24.2

Genomic location:

Preferred name:

NM_000130.4(F5):c.1601G>A (p.Arg534Gln)

Other names:

F5, ARG506GLN; F5:c.1601G>A (p.Arg534Gln)

HGVS:

NC_000001.11:g.169549811C>T
NG_011806.1:g.41721G>A
NM_000130.4:c.1601G>A
NP_000121.2:p.Arg534Gln
LRG_553t1:c.1601G>A
LRG_553:g.41721G>A
LRG_553p1:p.Arg534Gln
NC_000001.10:g.169519049T=
NG_011806.1:c.1601G>A
p.Arg506Gln

Protein change:

R506Q; ARG506GLN

Links:

OMIM: 612309.0001; dbSNP: rs6025

GMAF:

0.0060(T), 6025

NCBI 1000 Genomes Browser:

rs6025

Allele Frequency:

0.0214, GO-ESP

Molecular consequence:

NM_000130.4:c.1601G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Factor V deficiency
Synonyms:: LABILE FACTOR DEFICIENCY; OWREN PARAHEMOPHILIA; PARAHEMOPHILIA
Identifiers:: MedGen: C0015499; Orphanet: 326; OMIM: 227400
Age of onset:: All ages
Prevalence:: 1-9 / 1 000 000 326

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000262346	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 6, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000262346

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 6, 2015)

germline

clinical testing

Citation Link

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

Details of each submission

From Invitae, SCV000262346.1

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

Description

This sequence change replaces arginine with gluatmine at codon 534 of the F5 protein (p.Arg534Gln). The arginine residue is weakly conserved and there is a small physicochemical difference between arginine and glutamine. This variant, also known as Factor V Leiden mutation, is a well documented and common cause of activated protein C resistance (PMID: 8164741, 7910348). This variant has also been reported as R506Q. This variant disrupts the activated protein C cleavage site in the F5 protein and leads to a defective anticoagulant response in vitro (PMID: 7911872, 7910348). For these reasons, this variant has been classified as Pathogenic.

#	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: Apr 19, 2016

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