BGLAP

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

Basic information

Region (hg38): 1:156242183-156243317

Links

ENSG00000242252 ∙ NCBI:632 ∙ OMIM:112260 ∙ HGNC:1043 ∙ Uniprot:P02818 ∙ 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 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	1		2
missense			5		1	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)
1-156242556-C-T		not specified	Uncertain significance (May 31, 2023)
1-156242567-G-A		not specified	Uncertain significance (Mar 06, 2023)
1-156242577-C-A		not specified	Uncertain significance (Sep 22, 2022)
1-156242814-C-G		not specified	Uncertain significance (Mar 02, 2023)
1-156242823-A-G		not specified	Uncertain significance (Jul 20, 2021)
1-156243037-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-156243120-C-G		not specified	Uncertain significance (Aug 21, 2023)
1-156243121-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-156243139-C-T		not specified	Uncertain significance (Jun 28, 2022)
1-156243140-G-A			Benign (Dec 31, 2019)
1-156243151-G-A		not specified	Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BGLAP	protein_coding	protein_coding	ENST00000368272	4	1360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.62e-8	0.0338	125663	1	74	125738	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	56	63.5	0.882	0.00000408	624
Missense in Polyphen		24	21.29	1.1273		194
Synonymous	-1.06	37	29.6	1.25	0.00000228	196
Loss of Function	-1.58	9	5.13	1.75	2.17e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000403	0.000401
Ashkenazi Jewish	0.00330	0.00288
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000344	0.000334
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

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

• 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

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

Mouse Genome Informatics

• Gene name: Bglap3

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