BGLAP
Basic information
Region (hg38): 1:156242184-156243317
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 2 | |||||
missense | 9 | |||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 10 | 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:
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:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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