rs1085307183

Positions:

• chr2-202464972-A-AT

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1 PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_001204.7(BMPR2):c.240_241insT (p.Lys81Ter) variant is a DNA single thymine base insertion predicted to cause a frameshift, replacing a lysine residue for a stop codon at position 81. The variant is absent from the gnomAD v.2.1.1 controls and v3.0 (PM2_supporting). c.240_241insT was found in a patient with pulmonary arterial hypertension (PMID:20496075). The variant resides in the second exon of BMPR2 and generates a stop codon that is predicted to cause nonsense-mediated decay (PVS1). In summary, this variant meets the criteria to be classified as likely pathogenic for pulmonary arterial hypertension based on ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: PM2_supporting, PVS1 (VCEP specification version v 1.1, 1/18/2024). LINK:https://erepo.genome.network/evrepo/ui/classification/CA645293999/MONDO:0015924/125

• Frequency: Genomes: not found (cov: 32)
• Consequence: BMPR2 NM_001204.7 frameshift, stop_gained
• Clinical Significance: Likely pathogenic reviewed by expert panel P:2
• Conservation: PhyloP100: 5.80

Genes affected

BMPR2 (HGNC:1078): (bone morphogenetic protein receptor type 2) This gene encodes a member of the bone morphogenetic protein (BMP) receptor family of transmembrane serine/threonine kinases. The ligands of this receptor are members of the TGF-beta superfamily. BMPs are involved in endochondral bone formation and embryogenesis. These proteins transduce their signals through the formation of heteromeric complexes of two different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Mutations in this gene have been associated with primary pulmonary hypertension, both familial and fenfluramine-associated, and with pulmonary venoocclusive disease. [provided by RefSeq, May 2020]

BMPR2 (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMPR2	NM_001204.7	c.240_241insT	p.Lys81fs	frameshift_variant, stop_gained	2/13	ENST00000374580.10	NP_001195.2
BMPR2	XM_011511687.2	c.240_241insT	p.Lys81fs	frameshift_variant, stop_gained	2/13		XP_011509989.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BMPR2	ENST00000374580.10	c.240_241insT	p.Lys81fs	frameshift_variant, stop_gained	2/13	1	NM_001204.7	ENSP00000363708.4
BMPR2	ENST00000374574.2	c.240_241insT	p.Lys81fs	frameshift_variant, stop_gained	2/12	2		ENSP00000363702.2
BMPR2	ENST00000479069.1	n.147_148insT		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: reviewed by expert panel

Submissions by phenotype

Pulmonary arterial hypertension Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

Clingen Pulmonary Hypertension Variant Curation Expert Panel, ClinGen

May 03, 2024

The NM_001204.7(BMPR2):c.240_241insT (p.Lys81Ter) variant is a DNA single thymine base insertion predicted to cause a frameshift, replacing a lysine residue for a stop codon at position 81. The variant is absent from the gnomAD v.2.1.1 controls and v3.0 (PM2_supporting). c.240_241insT was found in a patient with pulmonary arterial hypertension (PMID:20496075). The variant resides in the second exon of BMPR2 and generates a stop codon that is predicted to cause nonsense-mediated decay (PVS1). In summary, this variant meets the criteria to be classified as likely pathogenic for pulmonary arterial hypertension based on ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: PM2_supporting, PVS1 (VCEP specification version v 1.1, 1/18/2024). -

Pulmonary hypertension, primary, 1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

Rare Disease Genomics Group, St George's University of London

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1085307183; hg19: chr2-203329695;