chr2-202464950-C-G

Position:

• chr2-202464950-C-G

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2_Supporting PS4_Supporting

This summary comes from the ClinGen Evidence Repository: The c.218C>G, (p.Ser73Ter) (NM_001204.7) variant in BMPR2 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 2 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID:16429395). This variant has been reported in 2 pulmonary arterial hypertension probands (PS4_Supporting) (PMID:26387786 ; PMID:32581362). This variant is absent from gnomAD v2.1.1 controls (PM2_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP (specification version 11, 1/18/2024): PVS1, PS4_Supporting, PM2_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA278072/MONDO:0015924/125

• Frequency: Genomes: not found (cov: 32)
• Consequence: BMPR2 NM_001204.7 stop_gained
• Clinical Significance: Pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 3.01

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]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: 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.218C>G	p.Ser73Ter	stop_gained	2/13	ENST00000374580.10	NP_001195.2
BMPR2	XM_011511687.2	c.218C>G	p.Ser73Ter	stop_gained	2/13		XP_011509989.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BMPR2	ENST00000374580.10	c.218C>G	p.Ser73Ter	stop_gained	2/13	1	NM_001204.7	ENSP00000363708	P1
BMPR2	ENST00000374574.2	c.218C>G	p.Ser73Ter	stop_gained	2/12	2		ENSP00000363702
BMPR2	ENST00000479069.1	n.125C>G		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: reviewed by expert panel

Submissions by phenotype

Pulmonary arterial hypertension Pathogenic:2

Pathogenic, reviewed by expert panel	curation	Clingen Pulmonary Hypertension Variant Curation Expert Panel, ClinGen	May 03, 2024	The c.218C>G, (p.Ser73Ter) (NM_001204.7) variant in BMPR2 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 2 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 16429395). This variant has been reported in 2 pulmonary arterial hypertension probands (PS4_Supporting) (PMID: 26387786 ; PMID: 32581362). This variant is absent from gnomAD v2.1.1 controls (PM2_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP (specification version 11, 1/18/2024): PVS1, PS4_Supporting, PM2_Supporting. -
Pathogenic, no assertion criteria provided	research	NIHR Bioresource Rare Diseases, University of Cambridge	-	- -

Pulmonary hypertension, primary, 1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 01, 2000

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.62
CADD	Pathogenic	37
DANN	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Uncertain	0.95	D
MutationTaster	Benign	1.0	A;A
Vest4		0.94
GERP RS		5.5

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs137852742; hg19: chr2-203329673;