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

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 30, 2021)
Last evaluated:
Feb 1, 2019
Accession:
VCV000627022.10
Variation ID:
627022
Description:
single nucleotide variant
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NM_000129.3(F13A1):c.1777G>A (p.Gly593Ser)

Allele ID
615416
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6p25.1
Genomic location
6: 6167589 (GRCh38) GRCh38 UCSC
6: 6167822 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_549t1:c.1777G>A LRG_549p1:p.Gly593Ser
LRG_549:g.158103G>A
NC_000006.11:g.6167822C>T
... more HGVS
Protein change
G593S
Other names
-
Canonical SPDI
NC_000006.12:6167588:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00256
The Genome Aggregation Database (gnomAD) 0.00258
The Genome Aggregation Database (gnomAD), exomes 0.00190
Exome Aggregation Consortium (ExAC) 0.00175
1000 Genomes Project 0.00100
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00269
Links
dbSNP: rs138754417
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 3 criteria provided, single submitter Feb 1, 2017 RCV000998514.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Feb 1, 2019 RCV000851722.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
F13A1 - - GRCh38
GRCh37
162 200

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Feb 01, 2019)
criteria provided, single submitter
Method: research
Factor XIII, A subunit, deficiency of
Allele origin: unknown
NIHR Bioresource Rare Diseases, University of Cambridge
Study: ThromboGenomics
Accession: SCV000899557.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Factor XIII, A subunit, deficiency of
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001324283.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
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, … (more)
Uncertain significance
(Feb 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001154617.7
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959587.1
Submitted: (Sep 30, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001966470.1
Submitted: (Sep 21, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders. Downes K Blood 2019 PMID: 31064749
Identification of eight novel coagulation factor XIII subunit A mutations: implied consequences for structure and function. Ivaskevicius V Haematologica 2010 PMID: 20179087

Text-mined citations for rs138754417...

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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 Oct 07, 2021