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GeneBe

BMP7

bone morphogenetic protein 7, the group of Bone morphogenetic proteins

Basic information

Region (hg38): 20:57168752-57266641

Links

ENSG00000101144NCBI:655OMIM:112267HGNC:1074Uniprot:P18075AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • multiple congenital anomalies/dysmorphic syndrome (Moderate), mode of inheritance: AD
  • hypospadias (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BMP7 gene.

  • not provided (48 variants)
  • Inborn genetic diseases (16 variants)
  • BMP7-related condition (4 variants)
  • Congenital anomaly of kidney and urinary tract (3 variants)
  • Atrial septal defect 8 (1 variants)
  • Congenital total pulmonary venous return anomaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
2
clinvar
7
clinvar
9
missense
30
clinvar
2
clinvar
32
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
6
clinvar
21
clinvar
27
Total 1 0 30 8 30

Variants in BMP7

This is a list of pathogenic ClinVar variants found in the BMP7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
20-57171012-C-T BMP7-related condition Uncertain significance (Feb 16, 2023)2628678
20-57171040-G-A Benign (Jan 31, 2024)710157
20-57171051-T-G not specified Uncertain significance (Dec 12, 2022)2329451
20-57171059-G-A not specified Uncertain significance (Mar 01, 2023)2492663
20-57171099-T-C not specified Uncertain significance (Oct 31, 2023)2688672
20-57171260-T-C Benign (Dec 23, 2018)1273116
20-57173008-C-T Benign (Dec 23, 2018)1286946
20-57173048-A-AT Likely benign (Nov 26, 2019)1315742
20-57173150-G-A Benign (Jun 26, 2018)1242634
20-57173242-G-A BMP7-related condition Likely benign (Aug 11, 2020)3054580
20-57173256-C-A Uncertain significance (Jun 05, 2022)2066422
20-57173297-G-A not specified Uncertain significance (Jul 14, 2022)2298542
20-57173302-G-A Benign (Nov 13, 2023)2693746
20-57173646-CATAAA-C Benign (Jun 29, 2018)1249651
20-57174725-A-G Benign (Jun 29, 2018)1258246
20-57174925-C-T Benign (Jan 31, 2024)710158
20-57174945-C-T not specified Uncertain significance (Feb 27, 2024)3134562
20-57174980-G-C BMP7-related condition Uncertain significance (Jan 06, 2023)2629845
20-57174981-C-A not specified Uncertain significance (Nov 28, 2023)3134568
20-57174993-C-T not specified Uncertain significance (Dec 20, 2021)3134567
20-57175004-T-C Congenital total pulmonary venous return anomaly • BMP7-related condition Benign (Nov 27, 2023)771049
20-57175148-G-T Benign (Jun 28, 2018)1238833
20-57183425-CT-C Benign (Jun 26, 2018)1225889
20-57183506-C-T Benign (Aug 03, 2018)1291873
20-57183536-A-G Benign (Aug 03, 2018)1224759

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BMP7protein_codingprotein_codingENST00000395863 797882
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1270.8721257380101257480.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.781902730.6960.00001822841
Missense in Polyphen56113.520.493331196
Synonymous0.2361111140.9720.00000826807
Loss of Function2.90518.50.2719.60e-7189

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001280.000123
Ashkenazi Jewish0.000.00
East Asian0.00005540.0000544
Finnish0.000.00
European (Non-Finnish)0.00004490.0000439
Middle Eastern0.00005540.0000544
South Asian0.00006800.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Induces cartilage and bone formation. May be the osteoinductive factor responsible for the phenomenon of epithelial osteogenesis. Plays a role in calcium regulation and bone homeostasis.;
Pathway
TGF-beta signaling pathway - Homo sapiens (human);Axon guidance - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);TGF-Core;Neural Crest Differentiation;Endoderm Differentiation;Mesodermal Commitment Pathway;Differentiation of white and brown adipocyte;Lung fibrosis;Role of Osx and miRNAs in tooth development;Endochondral Ossification;alk in cardiac myocytes;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Extracellular matrix organization;Molecules associated with elastic fibres;Elastic fibre formation;TGF-beta super family signaling pathway canonical;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;BMP receptor signaling;GPCR signaling-G alpha i;BMP2 signaling TGF-beta MV;BMP signaling Dro;ALK2 signaling events (Consensus)

Recessive Scores

pRec
0.673

Intolerance Scores

loftool
0.123
rvis_EVS
-0.51
rvis_percentile_EVS
21.41

Haploinsufficiency Scores

pHI
0.994
hipred
Y
hipred_score
0.853
ghis
0.634

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.958

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bmp7
Phenotype
embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype; pigmentation phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype;

Zebrafish Information Network

Gene name
bmp7a
Affected structure
erythroid lineage cell
Phenotype tag
abnormal
Phenotype quality
absent

Gene ontology

Biological process
skeletal system development;ossification;metanephros development;ureteric bud development;mesoderm formation;mesonephros development;epithelial to mesenchymal transition;endocardial cushion formation;pericardium morphogenesis;axon guidance;embryonic pattern specification;regulation of signaling receptor activity;positive regulation of gene expression;negative regulation of striated muscle cell apoptotic process;positive regulation of epithelial to mesenchymal transition;positive regulation of peptidyl-threonine phosphorylation;positive regulation of pathway-restricted SMAD protein phosphorylation;dendrite development;neural fold elevation formation;embryonic limb morphogenesis;positive regulation of bone mineralization;BMP signaling pathway;epithelial cell differentiation;hindbrain development;negative regulation of NF-kappaB transcription factor activity;response to estradiol;response to vitamin D;positive regulation of heterotypic cell-cell adhesion;protein localization to nucleus;negative regulation of phosphorylation;odontogenesis of dentin-containing tooth;regulation of apoptotic process;positive regulation of apoptotic process;steroid hormone mediated signaling pathway;negative regulation of MAP kinase activity;regulation of MAPK cascade;response to peptide hormone;negative regulation of neuron differentiation;positive regulation of osteoblast differentiation;negative regulation of Notch signaling pathway;negative regulation of cell cycle;negative regulation of mitotic nuclear division;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;cell development;embryonic camera-type eye morphogenesis;cardiac muscle tissue development;branching morphogenesis of an epithelial tube;mesenchymal cell differentiation;neuron projection morphogenesis;cartilage development;pharyngeal system development;embryonic skeletal joint morphogenesis;regulation of pathway-restricted SMAD protein phosphorylation;SMAD protein signal transduction;cardiac septum morphogenesis;branching involved in salivary gland morphogenesis;mesenchyme development;negative regulation of cell death;negative regulation of prostatic bud formation;regulation of branching involved in prostate gland morphogenesis;chorio-allantoic fusion;heart trabecula morphogenesis;monocyte aggregation;cellular response to hypoxia;cellular response to BMP stimulus;negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis;negative regulation of glomerular mesangial cell proliferation;metanephric mesenchyme morphogenesis;nephrogenic mesenchyme morphogenesis;metanephric mesenchymal cell proliferation involved in metanephros development;positive regulation of dendrite development;positive regulation of hyaluranon cable assembly;negative regulation of NIK/NF-kappaB signaling;allantois development;positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis;regulation of removal of superoxide radicals
Cellular component
extracellular region;extracellular space;vesicle;collagen-containing extracellular matrix
Molecular function
cytokine activity;transforming growth factor beta receptor binding;protein binding;growth factor activity;heparin binding;BMP receptor binding