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.1257A>T (p.Arg419Ser)

CA350341975

425905 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
UUID: b13676af-48b9-4741-b597-97d48b933dbf
Approved on: 2025-01-03
Published on: 2025-01-03

HGVS expressions

NM_001204.7:c.1257A>T
NM_001204.7(BMPR2):c.1257A>T (p.Arg419Ser)
NC_000002.12:g.202532713A>T
CM000664.2:g.202532713A>T
NC_000002.11:g.203397436A>T
CM000664.1:g.203397436A>T
NC_000002.10:g.203105681A>T
NG_009363.1:g.161387A>T
ENST00000374580.10:c.1257A>T
ENST00000638587.1:c.1188A>T
ENST00000374574.2:c.1257A>T
ENST00000374580.8:c.1257A>T
NM_001204.6:c.1257A>T
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Uncertain Significance

Met criteria codes 2
PM1 PM2_Supporting
Not Met criteria codes 4
BA1 BS1 BP4 PP3

Evidence Links 0

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
BMPR2 c.1257A>T is a missense variant predicted to cause substitution of arginine to serine at amino acid position 419 (p.Arg419Ser). The variant is absent from gnomAD v2.1.1 controls and found at a maximum allele frequency of 0.000022 in gnomAD v4.1.0 in the East Asian ancestry group, meeting PM2_supporting criterion of <0.01% (BA1 and BS1 not met). The REVEL score of 0.59 does not meet BP4 (<=0.25) or PP3 (>=0.75) criteria. This variant resides within the critical kinase domain (PM1_moderate met). Co-segregation/case, experimental criteria, and alternative missense variants at the same location were not evaluated due to lack of reported evidence. 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: PM2_supporting, PM1_moderate (VCEP specification version 1.1.0, 1/18/2024).
Met criteria codes
PM1
This variant resides within the critical kinase domain but not is not a known critical residue, so PM1_moderate is met.
PM2_Supporting
The variant is absent from gnomAd v2.1.1 controls and with a maximum allele frequency of 0.000022 in gnomAD v4.1.0 in the East Asian ancestry group, meeting PM2_supporting criterion of <0.01%.
Not Met criteria codes
BA1
The variant is absent from gnomAd v2.1.1 controls and with a maximum allele frequency of 0.000022 in gnomAD v4.1.0 in the East Asian ancestry group, meeting PM2_supporting criterion of <0.01%.
BS1
The variant is absent from gnomAd v2.1.1 controls and with a maximum allele frequency of 0.000022 in gnomAD v4.1.0 in the East Asian ancestry group, meeting PM2_supporting criterion of <0.01%.
BP4
REVEL score of 0.59 does not meet BP4 (<=0.25) or PP3 (>=0.75) criteria.
PP3
REVEL score of 0.59 does not meet BP4 (<=0.25) or PP3 (>=0.75) criteria.
Curation History
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