2-202464832-T-C

Position:

• chr2-202464832-T-C

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM5_Supporting PP3 PM2_Supporting PS4_Supporting PS3 PM1_Strong

This summary comes from the ClinGen Evidence Repository: The NM_001204.7(BMPR2) c.100T>C variant is a missense variant predicted to cause a cysteine to arginine substitution at amino acid position 34 (p.Cys34Arg). The variant is absent from gnomAD v.2.1.1 and v4.1 (PM2_supporting) and has been reported in two unrelated PAH probands (PMID:29650961) (PS4_supporting). The variant is located within the extracellular ligand-binding domain and p.Cys34 is a critical residue for protein function (PM1_strong). Two additional likely pathogenic variants, c.101G>T (p.Cys34Phe) and c.102T>G (p.Cys34Trp) have been reported at the same residue (PMID:27453251, PMID:30578397) (PM5_supporting). HeLa cells transfected with a BMPR2 p.C34R construct demonstrated that the mutant protein is mislocalized in the cell and does not reach the plasma membrane, with some retention in the ER/Golgi (PMID:25688877) (PS3). In silico prediction (REVEL = 0.939) is consistent with a pathogenic effect for this variant (PP3). In summary, the 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: PS3, PS4_supporting, PM1_strong, PM2_supporting, PM5_supporting, PP3 (VCEP specification version v 1.1, 1/18/2024). LINK:https://erepo.genome.network/evrepo/ui/classification/CA350399040/MONDO:0015924/125

• Frequency: Genomes: not found (cov: 32)
• Consequence: BMPR2 NM_001204.7 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 6.51

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 12 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMPR2	NM_001204.7	c.100T>C	p.Cys34Arg	missense_variant	2/13	ENST00000374580.10
BMPR2	XM_011511687.2	c.100T>C	p.Cys34Arg	missense_variant	2/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMPR2	ENST00000374580.10	c.100T>C	p.Cys34Arg	missense_variant	2/13	1	NM_001204.7	P1
BMPR2	ENST00000374574.2	c.100T>C	p.Cys34Arg	missense_variant	2/12	2
BMPR2	ENST00000479069.1	n.7T>C		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, no assertion criteria provided	research	NIHR Bioresource Rare Diseases, University of Cambridge	-	- -
Pathogenic, reviewed by expert panel	curation	Clingen Pulmonary Hypertension Variant Curation Expert Panel, ClinGen	Sep 20, 2024	The NM_001204.7(BMPR2) c.100T>C variant is a missense variant predicted to cause a cysteine to arginine substitution at amino acid position 34 (p.Cys34Arg). The variant is absent from gnomAD v.2.1.1 and v4.1 (PM2_supporting) and has been reported in two unrelated PAH probands (PMID: 29650961) (PS4_supporting). The variant is located within the extracellular ligand-binding domain and p.Cys34 is a critical residue for protein function (PM1_strong). Two additional likely pathogenic variants, c.101G>T (p.Cys34Phe) and c.102T>G (p.Cys34Trp) have been reported at the same residue (PMID: 27453251, PMID: 30578397) (PM5_supporting). HeLa cells transfected with a BMPR2 p.C34R construct demonstrated that the mutant protein is mislocalized in the cell and does not reach the plasma membrane, with some retention in the ER/Golgi (PMID: 25688877) (PS3). In silico prediction (REVEL = 0.939) is consistent with a pathogenic effect for this variant (PP3). In summary, the 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: PS3, PS4_supporting, PM1_strong, PM2_supporting, PM5_supporting, PP3 (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

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D;.;.
Eigen	Pathogenic	0.72
Eigen_PC	Pathogenic	0.71
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.81	T;T;T
M_CAP	Pathogenic	0.82	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Uncertain	2.0	M;M;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-6.2	D;D;.
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	D;D;.
Sift4G	Uncertain	0.020	D;D;.
Polyphen		1.0	D;.;.
Vest4		0.97
MutPred		0.95		Loss of sheet (P = 0.0054);Loss of sheet (P = 0.0054);.;
MVP		1.0
MPC		1.5
ClinPred		1.0	D
GERP RS		5.4
Varity_R		0.98
gMVP		0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs1085307163; hg19: chr2-203329555;