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 label mismatch: BMPR2 vs undefined
  • 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.1259G>A (p.Cys420Tyr)

CA350341979

425907 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
UUID: 0a8bb83a-1de5-4a7c-b64a-d879928274f0
Approved on: 2025-04-29
Published on: 2025-04-29

HGVS expressions

NM_001204.7:c.1259G>A
NM_001204.7(BMPR2):c.1259G>A (p.Cys420Tyr)
NC_000002.12:g.202532715G>A
CM000664.2:g.202532715G>A
NC_000002.11:g.203397438G>A
CM000664.1:g.203397438G>A
NC_000002.10:g.203105683G>A
NG_009363.1:g.161389G>A
ENST00000374580.10:c.1259G>A
ENST00000638587.1:c.1190G>A
ENST00000374574.2:c.1259G>A
ENST00000374580.8:c.1259G>A
NM_001204.6:c.1259G>A
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PM5 PM1 PS4_Moderate
Not Met criteria codes 1
BP4

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.1259G>A is a missense variant predicted to cause substitution of cysteine to tyrosine at amino acid position 420 (p.Cys420Tyr). The variant is absent from gnomAD v2.1.1 and v4.1 (PM2_supporting). A REVEL score of 0.924 meets PP3_supporting (>0.75). This variant resides within the conserved catalytic kinase domain but does not affect a known critical residue (PM1_moderate). The variant has been reported in four unrelated PAH probands (PMID: 15146475, 16429395, 21737554) with additional citations referring back to the same individuals (PMID: 21801371, 32634488, 30578397) (PS4_moderate). A different missense variant at the same amino acid residue, p.Cys420Arg (PMID: 11115378, 21801371) was previously classified by the PH VCEP as pathogenic (PM5_moderate). In summary, this variant meets the criteria to be classified as a likely pathogenic variant for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: PS4_moderate, PM1_moderate, PM5_moderate, PM2_supporting, PP3_supporting (VCEP specification version 1.1, 1/18/2024).
Met criteria codes
PM2_Supporting
Absent from gnomad v2.1.1 and v4.1.0.
PP3
REVEL = 0.924, above the threshold of >=0.75.
PM5
c.1258T>C; p.Cys420Arg (PMID: 11115378, 21801371) was previously classified by the PH VCEP as pathogenic.
PM1
Located in the conserved catalytic kinase domain but not a known critical residue.
PS4_Moderate
The variant has been reported in four unrelated PAH probands (PMID: 15146475, 16429395, 21737554) with additional citations referring back to the same individuals (PMID: 21801371, 32634488, 30578397).
Not Met criteria codes
BP4
REVEL = 0.924, above the threshold of >=0.75.
Curation History
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