BMP5

bone morphogenetic protein 5, the group of Bone morphogenetic proteins

Basic information

Region (hg38): 6:55753653-55875590

Links

ENSG00000112175 ∙ NCBI:653 ∙ OMIM:112265 ∙ HGNC:1072 ∙ Uniprot:P22003 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BMP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP5 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				3	3	6
missense			27	2	2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				4		4
Total	0	0	27	9	5

Variants in BMP5

This is a list of pathogenic ClinVar variants found in the BMP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-55755552-C-T		not specified	Uncertain significance (Jul 27, 2021)
6-55755559-C-T		not specified	Uncertain significance (Oct 06, 2022)
6-55755594-C-G		not specified	Uncertain significance (May 31, 2023)
6-55755658-C-T		not specified	Uncertain significance (Nov 10, 2022)
6-55759017-T-C		not specified	Uncertain significance (Nov 03, 2022)
6-55759042-T-C		not specified	Uncertain significance (Mar 17, 2023)
6-55759089-G-A		BMP5-related disorder	Benign (Jun 27, 2019)
6-55759124-TAC-T		BMP5-related disorder	Likely benign (Mar 22, 2019)
6-55759124-T-TAC		BMP5-related disorder	Likely benign (Jan 27, 2020)
6-55759124-T-TACACAC		BMP5-related disorder	Benign (Jul 31, 2018)
6-55759124-T-TACACACACAC		BMP5-related disorder	Likely benign (Mar 06, 2019)
6-55760454-TA-T		Microtia;Hypoplastic ischiopubic ramus;Patellar aplasia;Atrioventricular canal defect	Likely pathogenic (May 01, 2024)
6-55760493-G-A		BMP5-related disorder	Benign (Jun 29, 2018)
6-55760519-C-T		not specified	Uncertain significance (Jun 01, 2023)
6-55760520-A-C		BMP5-related disorder	Uncertain significance (Oct 11, 2022)
6-55760530-T-C		not specified	Uncertain significance (Aug 23, 2021)
6-55774100-G-A		not specified	Uncertain significance (Feb 07, 2023)
6-55774112-T-C		not specified	Uncertain significance (Oct 24, 2023)
6-55774120-T-C		not specified	Uncertain significance (Dec 13, 2022)
6-55774158-C-A		not specified	Uncertain significance (Aug 12, 2021)
6-55774163-A-G		not specified	Uncertain significance (Dec 13, 2022)
6-55774182-T-C		BMP5-related disorder	Likely benign (Apr 10, 2019)
6-55774182-T-G		not specified	Uncertain significance (Sep 22, 2021)
6-55774201-T-C		not specified	Uncertain significance (Apr 22, 2022)
6-55774205-T-C		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMP5	protein_coding	protein_coding	ENST00000370830	7	121920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000901	0.997	125728	0	17	125745	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.625	228	256	0.890	0.0000144	2993
Missense in Polyphen		63	94.471	0.66687		1131
Synonymous	0.0172	87	87.2	0.998	0.00000468	863
Loss of Function	2.64	9	22.5	0.400	0.00000136	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces cartilage and bone formation.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);alk in cardiac myocytes;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;TGF-beta super family signaling pathway canonical;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;BMP2 signaling TGF-beta MV;BMP signaling Dro (Consensus)

Recessive Scores

• pRec: 0.260

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.929
• hipred: N
• hipred_score: 0.495
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.406

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bmp5
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system 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; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: bmp5
• Affected structure: perineuronal satellite cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: skeletal system development;ossification;endocardial cushion formation;type B pancreatic cell development;pericardium morphogenesis;pattern specification process;positive regulation of cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;negative regulation of epithelial to mesenchymal transition;positive regulation of pathway-restricted SMAD protein phosphorylation;negative regulation of steroid biosynthetic process;neural fold elevation formation;BMP signaling pathway;male genitalia development;hindbrain development;negative regulation of aldosterone biosynthetic process;regulation of apoptotic process;regulation of MAPK cascade;negative regulation of insulin-like growth factor receptor signaling pathway;ear development;positive regulation of transcription by RNA polymerase II;cell development;cardiac muscle tissue development;positive regulation of epithelial cell proliferation;cartilage development;pharyngeal system development;SMAD protein signal transduction;cardiac septum morphogenesis;chorio-allantoic fusion;heart trabecula morphogenesis;negative regulation of mononuclear cell migration;anterior head development;positive regulation of dendrite development;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;allantois development;negative regulation of cortisol biosynthetic process
• Cellular component: cellular_component;extracellular space;vesicle
• Molecular function: cytokine activity;transforming growth factor beta receptor binding;growth factor activity;BMP receptor binding