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.1202T>C (p.Leu401Ser)

CA350341841

425892 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
UUID: e5c447ba-d798-4f6f-b36c-f8610515e2b5
Approved on: 2025-01-03
Published on: 2025-01-03

HGVS expressions

NM_001204.7:c.1202T>C
NM_001204.7(BMPR2):c.1202T>C (p.Leu401Ser)
NC_000002.12:g.202532658T>C
CM000664.2:g.202532658T>C
NC_000002.11:g.203397381T>C
CM000664.1:g.203397381T>C
NC_000002.10:g.203105626T>C
NG_009363.1:g.161332T>C
ENST00000374580.10:c.1202T>C
ENST00000638587.1:c.1133T>C
ENST00000374574.2:c.1202T>C
ENST00000374580.8:c.1202T>C
NM_001204.6:c.1202T>C
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Uncertain Significance

Met criteria codes 2
PM1 PM2_Supporting
Not Met criteria codes 7
PS4 PS2 BA1 PP3 PM6 BS1 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
The c.1202T>C (p.Leu401Ser) variant is a missense variant harboured in exon 9 of the BMPR2 gene, predicted to cause substitution of leucine to serine encoding the functionally relevant catalytic kinase domain but without functional evidence indicating either critical or non-critical amino acid residue (PM1_moderate). This variant is absent from gnomAD v2.1.1 (controls) and v4.1 (PM2_supporting). The REVEL prediction algorithm score is 0.72, below the PH VCEP threshold of >=0.75 for pathogenicity but above the threshold of <=0.25 for benignity (PP3 and BP4 not met). The variant has been identified in a single individual with hereditary PAH, included in two reports (PMID: 32581362 and PMID: 16429395) (PS4 not met). The variant was paternally inherited (PS2 not met). Functional studies have not been conducted for this variant (PS3 not assessed). In summary, this variant meets the criteria to be classified as a variant of unknown significance for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: PM1_moderate, PM2_supporting, PP3_not met (VCEP specification version 1.1.0, 1/18/2024)
Met criteria codes
PM1
p.Tyr407Ser is located in the catalytic kinase domain.
PM2_Supporting
The variant is absent from gnomAD v2.1.1 controls and v4.1.
Not Met criteria codes
PS4
The variant was identified in a single individual diagnosed with hereditary PAH.
PS2
The variant was paternally inherited.
BA1
The variant is absent from gnomAD v2.1.1 controls and v4.1.
PP3
The REVEL score of 0.72 is below the PH VCEP threshold of >=0.75 for pathogenicity and above the threshold of <=0.25 for benignity.
PM6
The variant was paternally inherited.
BS1
The variant is absent from gnomAD v2.1.1 controls and v4.1.
BP4
The REVEL score of 0.72 is below the PH VCEP threshold of >=0.75 for pathogenicity and above the threshold of <=0.25 for benignity.
Curation History
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