BMP7

bone morphogenetic protein 7, the group of Bone morphogenetic proteins

Basic information

Region (hg38): 20:57168752-57266641

Links

ENSG00000101144 ∙ NCBI:655 ∙ OMIM:112267 ∙ HGNC:1074 ∙ Uniprot:P18075 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	7	9
missense			30		2	32
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding				6	21	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 disorder	Uncertain significance (Feb 16, 2023)
20-57171040-G-A			Benign (Jan 31, 2024)
20-57171051-T-G		not specified	Uncertain significance (Dec 12, 2022)
20-57171059-G-A		not specified	Uncertain significance (Mar 01, 2023)
20-57171099-T-C		not specified	Uncertain significance (Oct 31, 2023)
20-57171260-T-C			Benign (Dec 23, 2018)
20-57173008-C-T			Benign (Dec 23, 2018)
20-57173048-A-AT			Likely benign (Nov 26, 2019)
20-57173150-G-A			Benign (Jun 26, 2018)
20-57173242-G-A		BMP7-related disorder	Likely benign (Aug 11, 2020)
20-57173256-C-A			Uncertain significance (Jun 05, 2022)
20-57173297-G-A		not specified	Uncertain significance (Jul 14, 2022)
20-57173302-G-A			Benign (Nov 13, 2023)
20-57173646-CATAAA-C			Benign (Jun 29, 2018)
20-57174725-A-G			Benign (Jun 29, 2018)
20-57174925-C-T			Benign (Jan 31, 2024)
20-57174945-C-T		not specified	Uncertain significance (Feb 27, 2024)
20-57174980-G-C		BMP7-related disorder	Uncertain significance (Jan 06, 2023)
20-57174981-C-A		not specified	Uncertain significance (Nov 28, 2023)
20-57174993-C-T		not specified	Uncertain significance (Dec 20, 2021)
20-57175004-T-C		Congenital total pulmonary venous return anomaly • BMP7-related disorder	Benign (Nov 27, 2023)
20-57175148-G-T			Benign (Jun 28, 2018)
20-57183425-CT-C			Benign (Jun 26, 2018)
20-57183506-C-T			Benign (Aug 03, 2018)
20-57183536-A-G			Benign (Aug 03, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMP7	protein_coding	protein_coding	ENST00000395863	7	97882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.127	0.872	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	190	273	0.696	0.0000182	2841
Missense in Polyphen		56	113.52	0.49333		1196
Synonymous	0.236	111	114	0.972	0.00000826	807
Loss of Function	2.90	5	18.5	0.271	9.60e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000439
Middle Eastern	0.0000554	0.0000544
South Asian	0.0000680	0.0000653
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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