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GeneBe

BGLAP

bone gamma-carboxyglutamate protein, the group of Gla domain containing

Basic information

Region (hg38): 1:156242183-156243317

Links

ENSG00000242252NCBI:632OMIM:112260HGNC:1043Uniprot:P02818AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (6 variants)
  • not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BGLAP 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
clinvar
2
missense
5
clinvar
1
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 6 1 1

Variants in BGLAP

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

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

Position Type Phenotype Significance ClinVar
1-156242282-C-T Likely benign (Mar 01, 2022)2639450
1-156242577-C-A Inborn genetic diseases Uncertain significance (Sep 22, 2022)2312765
1-156242823-A-G Inborn genetic diseases Uncertain significance (Jul 20, 2021)2238715
1-156243120-C-G Inborn genetic diseases Uncertain significance (Aug 21, 2023)2620346
1-156243121-G-A Inborn genetic diseases Uncertain significance (Aug 11, 2022)2306547
1-156243139-C-T Inborn genetic diseases Uncertain significance (Jun 28, 2022)2205587
1-156243140-G-A Benign (Dec 31, 2019)780264
1-156243151-G-A Inborn genetic diseases Uncertain significance (Jan 31, 2022)2374800

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BGLAPprotein_codingprotein_codingENST00000368272 41360
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.62e-80.03381256631741257380.000298
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3345663.50.8820.00000408624
Missense in Polyphen2421.291.1273194
Synonymous-1.063729.61.250.00000228196
Loss of Function-1.5895.131.752.17e-761

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004030.000401
Ashkenazi Jewish0.003300.00288
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0003440.000334
Middle Eastern0.000.00
South Asian0.000.00
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Constitutes 1-2% of the total bone protein. It binds strongly to apatite and calcium.;
Pathway
Warfarin Pathway, Pharmacodynamics;Interleukin-11 Signaling Pathway;Vitamin D Receptor Pathway;Osteoblast Signaling;RUNX2 regulates osteoblast differentiation;RUNX2 regulates bone development;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;RNA Polymerase II Transcription;Gamma-carboxylation of protein precursors;Removal of aminoterminal propeptides from gamma-carboxylated proteins;Gamma-carboxylation, transport, and amino-terminal cleavage of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Glucocorticoid receptor regulatory network;Notch-mediated HES/HEY network;Validated transcriptional targets of AP1 family members Fra1 and Fra2;Regulation of retinoblastoma protein;FGF signaling pathway (Consensus)

Recessive Scores

pRec
0.262

Intolerance Scores

loftool
0.641
rvis_EVS
0.48
rvis_percentile_EVS
79.04

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.213
ghis
0.500

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bglap3
Phenotype

Gene ontology

Biological process
skeletal system development;ossification;osteoblast differentiation;osteoblast development;endoplasmic reticulum to Golgi vesicle-mediated transport;cell adhesion;cell aging;response to mechanical stimulus;response to gravity;response to zinc ion;response to activity;bone mineralization;regulation of bone mineralization;response to vitamin K;response to vitamin D;response to testosterone;response to hydroxyisoflavone;odontogenesis;response to estrogen;regulation of bone resorption;response to ethanol;regulation of osteoclast differentiation;response to glucocorticoid;bone development;cellular response to vitamin D;cellular response to growth factor stimulus;regulation of cellular response to insulin stimulus
Cellular component
extracellular region;extracellular space;cytoplasm;endoplasmic reticulum lumen;rough endoplasmic reticulum;Golgi lumen;dendrite;vesicle;perikaryon
Molecular function
structural molecule activity;calcium ion binding;structural constituent of bone;hydroxyapatite binding