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NM_001204.7(BMPR2):c.1516A>G (p.Met506Val) AND Pulmonary arterial hypertension

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 1, 2024
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV004551612.1

Allele description [Variation Report for NM_001204.7(BMPR2):c.1516A>G (p.Met506Val)]

NM_001204.7(BMPR2):c.1516A>G (p.Met506Val)

Gene:
BMPR2:bone morphogenetic protein receptor type 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q33.2
Genomic location:
Preferred name:
NM_001204.7(BMPR2):c.1516A>G (p.Met506Val)
Other names:
NM_001204.7(BMPR2):c.1516A>G; p.Met506Val
HGVS:
  • NC_000002.12:g.202552818A>G
  • NG_009363.1:g.181492A>G
  • NM_001204.7:c.1516A>GMANE SELECT
  • NP_001195.2:p.Met506Val
  • LRG_712t1:c.1516A>G
  • LRG_712:g.181492A>G
  • NC_000002.11:g.203417541A>G
  • NM_001204.6:c.1516A>G
Protein change:
M506V
Links:
dbSNP: rs370457339
NCBI 1000 Genomes Browser:
rs370457339
Molecular consequence:
  • NM_001204.7:c.1516A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Pulmonary arterial hypertension
Identifiers:
MONDO: MONDO:0015924; MeSH: D000081029; MedGen: C2973725; Orphanet: 182090; Human Phenotype Ontology: HP:0002092

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005043320Clingen Pulmonary Hypertension Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen PH ACMG Specifications BMPR2 V1.1.0)		Uncertain Significance
(May 1, 2024) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From Clingen Pulmonary Hypertension Variant Curation Expert Panel, ClinGen, SCV005043320.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The BMPR2 c.1516A>G variant is a missense variant predicted to cause substitution of methionine to valine at amino acid position 506 ((p.(Met506Val)). The highest population minor allele frequency is for East Asian (0.00022) in gnomAD v2.1.1 controls and 0.00015 in gnomAD v3.1.2 and does not meet population criteria (PM2 <0.01%, BS1 >0.1%, anBA1 >1%). BP4 is met by the computational predictor REVEL score of 0.23, which is below the PH-VCEP specified threshold of <0.25 (additional support for BP4 is alpha missense score of 0.077). This variant does not reside within the critical extracellular or kinase domains, so PM1 is not met. Co-segregation/case and experimental criteria was not evaluated due to lack of reported evidence. Alternative variants in the same amino acid have not been reported. In summary, this variant meets the criteria to be classified as a variant of uncertain significance (VUS) for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: BP4 (VCEP specification version 1.1, 1/18/2024).

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

Last Updated: Sep 29, 2024