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GeneBe

BMP5

bone morphogenetic protein 5, the group of Bone morphogenetic proteins

Basic information

Region (hg38): 6:55753652-55875590

Links

ENSG00000112175NCBI:653OMIM:112265HGNC:1072Uniprot:P22003AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (22 variants)
  • not provided (4 variants)
  • BMP5-related condition (1 variants)

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
1
clinvar
1
missense
23
clinvar
2
clinvar
25
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 23 0 4

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)2371064
6-55755559-C-T not specified Uncertain significance (Oct 06, 2022)2215118
6-55755594-C-G not specified Uncertain significance (May 31, 2023)2554474
6-55755658-C-T not specified Uncertain significance (Nov 10, 2022)2381687
6-55759017-T-C not specified Uncertain significance (Nov 03, 2022)2322385
6-55759042-T-C not specified Uncertain significance (Mar 17, 2023)2526516
6-55759089-G-A BMP5-related condition Benign (Jun 27, 2019)3042737
6-55759124-TAC-T BMP5-related condition Likely benign (Mar 22, 2019)3038228
6-55759124-T-TAC BMP5-related condition Likely benign (Jan 27, 2020)3060530
6-55759124-T-TACACAC BMP5-related condition Benign/Likely benign (Mar 12, 2019)735236
6-55759124-T-TACACACACAC BMP5-related condition Likely benign (Mar 06, 2019)3037354
6-55760493-G-A BMP5-related condition Benign/Likely benign (Feb 28, 2019)708435
6-55760519-C-T not specified Uncertain significance (Jun 01, 2023)2554865
6-55760520-A-C BMP5-related condition Uncertain significance (Oct 11, 2022)2637076
6-55760530-T-C not specified Uncertain significance (Aug 23, 2021)2377696
6-55774100-G-A not specified Uncertain significance (Feb 07, 2023)2466472
6-55774112-T-C not specified Uncertain significance (Oct 24, 2023)3134550
6-55774120-T-C not specified Uncertain significance (Dec 13, 2022)3134549
6-55774158-C-A not specified Uncertain significance (Aug 12, 2021)2244275
6-55774163-A-G not specified Uncertain significance (Dec 13, 2022)2410273
6-55774182-T-C BMP5-related condition Likely benign (Apr 10, 2019)3038083
6-55774182-T-G not specified Uncertain significance (Sep 22, 2021)2379633
6-55774201-T-C not specified Uncertain significance (Apr 22, 2022)2284691
6-55774205-T-C not specified Uncertain significance (Aug 02, 2023)2615444
6-55774230-G-A BMP5-related condition Benign (Nov 18, 2019)3060109

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BMP5protein_codingprotein_codingENST00000370830 7121920
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0009010.9971257280171257450.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6252282560.8900.00001442993
Missense in Polyphen6394.4710.666871131
Synonymous0.01728787.20.9980.00000468863
Loss of Function2.64922.50.4000.00000136241

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003010.000300
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00007930.0000791
Middle Eastern0.000.00
South Asian0.000.00
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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