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NM_001114753.3(ENG):c.1633G>A (p.Gly545Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000237022.5
Variation ID:
237022
Description:
single nucleotide variant
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NM_001114753.3(ENG):c.1633G>A (p.Gly545Ser)

Allele ID
240451
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.11
Genomic location
9: 127818173 (GRCh38) GRCh38 UCSC
9: 130580452 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_589:g.41596G>A
LRG_589t1:c.1633G>A LRG_589p1:p.Gly545Ser
LRG_589t2:c.1633G>A LRG_589p2:p.Gly545Ser
... more HGVS
Protein change
G545S, G363S
Other names
NP_001108225.1:p.G545S
Canonical SPDI
NC_000009.12:127818172:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00029
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD), exomes 0.00052
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00062
Trans-Omics for Precision Medicine (TOPMed) 0.00048
Exome Aggregation Consortium (ExAC) 0.00052
Links
ClinGen: CA5252712
UniProtKB: P17813#VAR_070302
dbSNP: rs142896669
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Dec 6, 2020 RCV000226902.7
Uncertain significance 1 criteria provided, single submitter Apr 25, 2016 RCV000454429.1
Uncertain significance 1 criteria provided, single submitter Jun 27, 2018 RCV000664173.1
Benign 1 criteria provided, single submitter Apr 28, 2017 RCV001166478.1
Pathogenic 1 no assertion criteria provided - RCV000488732.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ENG Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
594 891
LOC102723566 - - - GRCh38 - 273

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 25, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000539100.1
Submitted: (Apr 03, 2017)
Evidence details
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Likely benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary hemorrhagic telangiectasia
Allele origin: germline
Invitae
Accession: SCV000283530.7
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jun 27, 2018)
criteria provided, single submitter
Method: case-control
Pulmonary arterial hypertension associated with congenital heart disease
Allele origin: maternal
Wendy Chung Laboratory,Columbia University Medical Center
Accession: SCV000784732.1
Submitted: (Jun 27, 2018)
Evidence details
Publications
PubMed (1)
Benign
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary hemorrhagic telangiectasia type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001328859.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (3)
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)
Pathogenic
(-)
no assertion criteria provided
Method: literature only
Primary pulmonary hypertension
Allele origin: germline
Medical & Molecular Genetics Group,University of Lincoln
Accession: SCV000576357.1
Submitted: (Aug 25, 2015)
Evidence details
Publications
PubMed (2)

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
Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease. Zhu N Genome medicine 2018 PMID: 30029678
Pulmonary Arterial Hypertension: A Current Perspective on Established and Emerging Molecular Genetic Defects. Machado RD Human mutation 2015 PMID: 26387786
Mutation in BMPR2 Promoter: A 'Second Hit' for Manifestation of Pulmonary Arterial Hypertension? Viales RR PloS one 2015 PMID: 26167679
Hemodynamic and genetic analysis in children with idiopathic, heritable, and congenital heart disease associated pulmonary arterial hypertension. Pfarr N Respiratory research 2013 PMID: 23298310
Detection of a significant association between mutations in the ACVRL1 gene and hepatic involvement in German patients with hereditary haemorrhagic telangiectasia. Brakensiek K Clinical genetics 2008 PMID: 18498373

Text-mined citations for rs142896669...

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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 30, 2021