The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001204.7(BMPR2):c.1509A>C (p.Glu503Asp)

CA16610570

409828 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
UUID: 43fb2d44-b756-4904-9ef4-19f0070db7a5
Approved on: 2025-09-19
Published on: 2025-09-19

HGVS expressions

NM_001204.7:c.1509A>C
NM_001204.7(BMPR2):c.1509A>C (p.Glu503Asp)
NC_000002.12:g.202552811A>C
CM000664.2:g.202552811A>C
NC_000002.11:g.203417534A>C
CM000664.1:g.203417534A>C
NC_000002.10:g.203125779A>C
NG_009363.1:g.181485A>C
ENST00000374580.10:c.1509A>C
ENST00000638587.1:c.1440A>C
ENST00000374574.2:c.1509A>C
ENST00000374580.8:c.1509A>C
NM_001204.6:c.1509A>C
More

Uncertain Significance

Not Met criteria codes 8
PS1 PP3 PM5 PM1 PM2 BS3 BS1 BP4

Evidence Links 4

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Pulmonary Hypertension Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BMPR2 Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Pulmonary Hypertension VCEP
The NM_001204.7(BMPR2) c.1509A>C variant is a missense variant predicted to cause substitution of glutamate by aspartate at amino acid 503 (p.Glu503Asp). The highest population minor allele frequency in gnomAD v2.1.1 (controls) is 0.0001105 (1/9046 alleles) in East Asian population, which is higher than the ClinGen PH VCEP threshold (<0.01%) for PM2 but lower than the threshold (>0.1%) for BS1. Therefore, this variant does not meet either of these population criteria. The computational predictor REVEL gives a score of 0.662, which is neither above nor below the thresholds predicting a damaging or benign impact on BMPR2 function. The variant does not affect protein localization to the plasma membrane (PMID: 25688877) or cell viability (PMID: 30809644). A single luciferase assay demonstrated comparable canonical transcriptional activity to wild-type (PMID: 18321866). However, the lack of effect on canonical signaling in one assay without replication in an independent assay, did not provide conclusive evidence for non-criticality (BS3 not met). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: No criteria scored. (VCEP specifications version 1.1, 1/18/2024)
Not Met criteria codes
PS1
Amino acid change has not been reported previously
PP3
REVEL score is 0.662 so does not meet the threshold to be classified as deleterious (REVEL >0.75)
PM5
Amino acid residue has not been previously reported as mutated
PM1
Variant is located in the kinase domain but the mutated residue is not a critical amino acid as determined by evolutionary conservation and structural analysis (Hanks and Hunter, 1995; PMID: 7768349).

PM2
Allele frequency in the East Asian population (gnomAD v2.1.1 controls) is greater than 0.01% (MAF: 1/9046 = 0.00011)
BS3
Cells transfected with the p.E503D variant have no damaging effects on cellular localization (PMID: 25688877), transcriptional activity (PMID: 18321866), or cell viability (PMID: 30809644). However, the lack of effect on canonical signaling in one assay without replication in an independent assay, does not provide conclusive evidence for non-criticality.

BS1
Allele frequency is less than 0.1% in gnomAD v2.1.1 controls
BP4
REVEL score is 0.662 so does not meet the threshold to be classified as no impact on gene or gene product (REVEL <0.25).
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.