GeneBe

chr2-202466927-TTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACC-GTAAAGTA

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5

The NM_001204.7(BMPR2):​c.248-592_413delTTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACCinsGTAAAGTA​(p.Gly83fs) variant causes a frameshift, splice acceptor, splice region, synonymous, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

BMPR2
NM_001204.7 frameshift, splice_acceptor, splice_region, synonymous, intron

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.443
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-202466927-TTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACC-GTAAAGTA is Pathogenic according to our data. Variant chr2-202466927-TTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACC-GTAAAGTA is described in ClinVar as [Pathogenic]. Clinvar id is 425734.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BMPR2NM_001204.7 linkc.248-592_413delTTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACCinsGTAAAGTA p.Gly83fs frameshift_variant, splice_acceptor_variant, splice_region_variant, synonymous_variant, intron_variant Exon 3 of 13 ENST00000374580.10 NP_001195.2 Q13873-1
BMPR2XM_011511687.2 linkc.248-592_413delTTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACCinsGTAAAGTA p.Gly83fs frameshift_variant, splice_acceptor_variant, splice_region_variant, synonymous_variant, intron_variant Exon 3 of 13 XP_011509989.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BMPR2ENST00000374580.10 linkc.248-592_413delTTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACCinsGTAAAGTA p.Gly83fs frameshift_variant, splice_acceptor_variant, splice_region_variant, synonymous_variant, intron_variant Exon 3 of 13 1 NM_001204.7 ENSP00000363708.4 Q13873-1
BMPR2ENST00000374574.2 linkc.248-592_413delTTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACCinsGTAAAGTA p.Gly83fs frameshift_variant, splice_acceptor_variant, splice_region_variant, synonymous_variant, intron_variant Exon 3 of 12 2 ENSP00000363702.2 Q13873-2
BMPR2ENST00000479069.1 linkn.155-592_320delTTTGGTATAGACAAAAATGAAACCTTACTCTTGCTTTAATAATTCTTCGATTAGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGCTCAGGAGTTTGAGACCGGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTAAGGTAGGAGAATCGCTTGAACCCGGGAGGTGGAGATTGCAGTGAGCTGAGATCGTGCCATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCGCCTCAATAAATAAATAAATAATTCTTAGATTAATCATGCAGTTAAACCTTTTTTGGTGGCCTTTTCCCCCCCATGAAATGTCTTTGGTATCCTTTACCATTTTTCTGTTTCTTAAAAATATGTTTCCTGTTGATTTGCAAAACTGTTTCATAGCTTACACGTACTCTCACATTTATTGAAATTACTGCTTAGTTTGTTGTTTTTCTCTTAGTTTTCTTTATCATATTGTCTCCTTTTTTGTATTCATATTGATTTATAGGATGTTGGTCTCACATTGGAGATCCCCAAGAGTGTCACTATGAAGAATGTGTAGTAACTACCACTCCTCCCTCAATTCAGAATGGAACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGTCAACTTTACTGAGAATTTTCCACCTCCTGACACAACACCinsGTAAAGTA splice_acceptor_variant, splice_region_variant, intron_variant, non_coding_transcript_exon_variant Exon 2 of 3 3

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Pulmonary hypertension, primary, 1 Pathogenic:1
-
Rare Disease Genomics Group, St George's University of London
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1553503473; hg19: chr2-203331650; API