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GeneBe

BMP6

bone morphogenetic protein 6, the group of Bone morphogenetic proteins

Basic information

Region (hg38): 6:7726098-7881728

Previous symbols: [ "VGR" ]

Links

ENSG00000153162NCBI:654OMIM:112266HGNC:1073Uniprot:P22004AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hemochromatosis type 5 (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Iron overload, susceptibility toAD/ARGastrointestinalThe condition may involve increased risk of liver dysfunction, and awareness may allow preventative measures such as avoidance of other risk factors for hepatic dysfunctionGastrointestinal26582087; 28335084; 32464486

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BMP6 gene.

  • Inborn genetic diseases (28 variants)
  • not provided (6 variants)
  • Iron overload, susceptibility to (3 variants)
  • Premature ovarian failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP6 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
clinvar
3
missense
1
clinvar
27
clinvar
3
clinvar
1
clinvar
32
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 1 27 6 1

Variants in BMP6

This is a list of pathogenic ClinVar variants found in the BMP6 region.

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

Position Type Phenotype Significance ClinVar
6-7727022-G-A not specified Uncertain significance (Jun 18, 2021)2408245
6-7727038-G-A BMP6-related condition Benign (Jan 02, 2020)3058879
6-7727052-G-A not specified Uncertain significance (Dec 05, 2023)3134561
6-7727124-C-T not specified Uncertain significance (Aug 12, 2021)2243246
6-7727166-C-G not specified Uncertain significance (Dec 02, 2022)3134553
6-7727180-G-A BMP6-related condition Benign (Feb 22, 2019)3056390
6-7727194-A-C not specified Uncertain significance (Jun 12, 2023)2559481
6-7727220-C-T not specified Uncertain significance (Dec 14, 2023)3134554
6-7727235-C-T not specified Uncertain significance (Mar 28, 2022)2367395
6-7727238-C-T Iron overload, susceptibility to Likely benign (Aug 01, 2022)1801214
6-7727239-C-T not specified Uncertain significance (Sep 12, 2023)2602464
6-7727242-T-C Iron overload, susceptibility to Likely benign (Feb 01, 2024)1801215
6-7727244-C-T not specified Uncertain significance (Jun 24, 2022)2297367
6-7727289-G-C Iron overload, susceptibility to risk factor (Nov 28, 2022)1801217
6-7727289-G-GAGC BMP6-related condition Benign (Dec 24, 2019)3037636
6-7727292-C-G Iron overload, susceptibility to • BMP6-related condition Benign/Likely benign (Dec 01, 2022)1801216
6-7727294-G-A BMP6-related condition Benign (Mar 12, 2019)3056089
6-7727325-C-T not specified Uncertain significance (Mar 23, 2022)2279589
6-7727364-C-A Premature ovarian failure Likely pathogenic (Mar 02, 2020)929751
6-7727382-C-G not specified Uncertain significance (Jul 06, 2022)3134555
6-7727394-A-G not specified Likely benign (Apr 15, 2022)2349570
6-7727395-A-G not specified Uncertain significance (Nov 08, 2022)2323796
6-7727405-C-G not specified Uncertain significance (Oct 05, 2023)3134556
6-7727408-G-T Likely benign (Aug 01, 2023)2578994
6-7727410-C-A not specified Uncertain significance (Mar 06, 2023)3134557

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BMP6protein_codingprotein_codingENST00000283147 7154626
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7590.241125744041257480.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.033152681.180.00001533306
Missense in Polyphen130128.121.01471444
Synonymous-0.6601201111.080.000006571020
Loss of Function3.59422.30.1800.00000122239

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.00009930.0000992
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.000.00
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Induces cartilage and bone formation.;
Pathway
TGF-beta signaling pathway - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);TGF-Core;Vitamin D Receptor Pathway;Hfe effect on hepcidin production;Endochondral Ossification;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;BMP receptor signaling;GPCR signaling-G alpha i;BMP2 signaling TGF-beta MV;BMP signaling Dro (Consensus)

Recessive Scores

pRec
0.373

Intolerance Scores

loftool
0.0702
rvis_EVS
-0.34
rvis_percentile_EVS
30.56

Haploinsufficiency Scores

pHI
0.743
hipred
Y
hipred_score
0.777
ghis
0.498

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.936

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bmp6
Phenotype
growth/size/body region phenotype; reproductive system phenotype; skeleton phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;skeletal system development;osteoblast differentiation;eye development;kidney development;positive regulation of endothelial cell proliferation;endochondral ossification;type B pancreatic cell development;cellular iron ion homeostasis;inflammatory response;immune response;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of pathway-restricted SMAD protein phosphorylation;response to activity;positive regulation of bone mineralization;BMP signaling pathway;male genitalia development;positive regulation of lipopolysaccharide-mediated signaling pathway;response to magnesium ion;positive regulation of chondrocyte differentiation;positive regulation of aldosterone biosynthetic process;response to retinoic acid;regulation of apoptotic process;regulation of MAPK cascade;positive regulation of endothelial cell differentiation;positive regulation of neuron differentiation;positive regulation of osteoblast differentiation;positive regulation of transcription by RNA polymerase II;cell development;positive regulation of epithelial cell proliferation;positive regulation of protein secretion;cartilage development;response to glucocorticoid;positive regulation of SMAD protein signal transduction;SMAD protein signal transduction;multicellular organismal iron ion homeostasis;cellular response to mechanical stimulus;cellular response to iron ion;cellular response to BMP stimulus;positive regulation of aldosterone secretion
Cellular component
extracellular space;cytoplasm;vesicle
Molecular function
cytokine activity;transforming growth factor beta receptor binding;growth factor activity;protein heterodimerization activity;BMP receptor binding