NM_000129.3(F13A1):c.1777G>A (p.Gly593Ser) AND Factor XIII, A subunit, deficiency of

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(1);Uncertain significance(1) (Last evaluated: Feb 1, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000851722.2

Allele description [Variation Report for NM_000129.3(F13A1):c.1777G>A (p.Gly593Ser)]

NM_000129.3(F13A1):c.1777G>A (p.Gly593Ser)

Gene:
F13A1:coagulation factor XIII A chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p25.1
Genomic location:
Preferred name:
NM_000129.3(F13A1):c.1777G>A (p.Gly593Ser)
HGVS:
  • NC_000006.12:g.6167589C>T
  • NG_008107.1:g.158103G>A
  • NM_000129.3:c.1777G>A
  • NP_000120.2:p.Gly593Ser
  • LRG_549t1:c.1777G>A
  • LRG_549:g.158103G>A
  • LRG_549p1:p.Gly593Ser
  • NC_000006.11:g.6167822C>T
Protein change:
G593S
Links:
dbSNP: rs138754417
NCBI 1000 Genomes Browser:
rs138754417
Molecular consequence:
  • NM_000129.3:c.1777G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Factor XIII, A subunit, deficiency of
Synonyms:
Factor XIII subunit A deficiency; Reduced factor XIII, subunit A
Identifiers:
MONDO: MONDO:0013187; MedGen: C2750514; Orphanet: 331; OMIM: 613225; Human Phenotype Ontology: HP:0040233

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000899557NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomicscriteria provided, single submitter
Likely pathogenic
(Feb 1, 2019)
unknownresearch

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

SCV001324283Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Apr 27, 2017)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
Europeanunknownyes1not providednot provided1not providedresearch

Citations

PubMed

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

Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders.

Downes K, Megy K, Duarte D, Vries M, Gebhart J, Hofer S, Shamardina O, Deevi SVV, Stephens J, Mapeta R, Tuna S, Al Hasso N, Besser MW, Cooper N, Daugherty L, Gleadall N, Greene D, Haimel M, Martin H, Papadia S, Revel-Vilk S, Sivapalaratnam S, et al.

Blood. 2019 Dec 5;134(23):2082-2091. doi: 10.1182/blood.2018891192.

PubMed [citation]
PMID:
31064749
PMCID:
PMC6993014
See all PubMed Citations (3)

Details of each submission

From NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics, SCV000899557.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1European1not providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001324283.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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

Last Updated: Oct 6, 2021

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