NM_000131.4(F7):c.-55C>T AND Factor VII deficiency

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Feb 1, 2019
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:: RCV000851624.11

Allele description [Variation Report for NM_000131.4(F7):c.-55C>T]

NM_000131.4(F7):c.-55C>T

Gene:

F7:coagulation factor VII [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q34

Genomic location:

Preferred name:

NM_000131.4(F7):c.-55C>T

Other names:

F7, -55C-T

HGVS:

NC_000013.11:g.113105787C>T
NG_009262.1:g.4997C>T
NM_000131.4:c.-55C>T
LRG_554t1:c.-55C>T
LRG_554:g.4997C>T
NC_000013.10:g.113760101C>T

Nucleotide change:

-55C-T

Links:

OMIM: 613878.0017; dbSNP: rs1418012389

NCBI 1000 Genomes Browser:

rs1418012389

Molecular consequence:

NM_000131.4:c.-55C>T - upstream transcript variant - [Sequence Ontology: SO:0001986]

Condition(s)

Name:: Factor VII deficiency
Synonyms:: Factor 7 deficiency; F7 deficiency; Hypoproconvertinemia
Identifiers:: MONDO: MONDO:0002244; MeSH: D005168; MedGen: C0015503

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000033105	OMIM	no assertion criteria provided	Pathogenic (Dec 15, 2000)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000899392	NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 1, 2019)	unknown	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 31064749

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000033105

OMIM

no assertion criteria provided

Pathogenic
(Dec 15, 2000)

germline

literature only

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

SCV000899392

NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 1, 2019)

unknown

research

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
European	unknown	yes	1	not provided	not provided	1	not provided	research

Citations

PubMed

A new mutation in the HNF4 binding region of the factor VII promoter in a patient with severe factor VII deficiency.

Carew JA, Pollak ES, Lopaciuk S, Bauer KA.

Blood. 2000 Dec 15;96(13):4370-2.

PubMed [citation]

PMID:: 11110717

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000033105.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

Carew et al. (2000) described a 25-year-old Polish man with severe factor VII deficiency (227500) who was compound heterozygous for 2 mutations in the F7 gene. The paternal allele contained 3 structural gene abnormalities, and the maternal allele carried a C-to-T transition at position -55 relative to the translation start site. This mutation partially impeded binding of the transcriptional activator HNF4 (600281) to the F7 promoter while greatly reducing reporter gene expression in hepatic cells.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics, SCV000899392.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	European	1	not provided	not provided	research	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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