CALB1
Basic information
Region (hg38): 8:90058608-90095475
Previous symbols: [ "CALB" ]
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 CALB1 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 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 0 |
Variants in CALB1
This is a list of pathogenic ClinVar variants found in the CALB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-90060634-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| 8-90060698-G-A | Benign (May 21, 2018) | |||
| 8-90063143-A-G | not specified | Uncertain significance (May 30, 2023) | ||
| 8-90065899-A-G | not specified | Uncertain significance (Jan 08, 2024) | ||
| 8-90069022-G-A | Likely benign (Feb 13, 2018) | |||
| 8-90069211-C-A | not specified | Uncertain significance (Mar 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CALB1 | protein_coding | protein_coding | ENST00000265431 | 11 | 36868 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.243 | 0.757 | 125739 | 0 | 6 | 125745 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.44 | 87 | 134 | 0.649 | 0.00000628 | 1728 |
| Missense in Polyphen | 28 | 56.764 | 0.49327 | 763 | ||
| Synonymous | 0.683 | 47 | 53.3 | 0.881 | 0.00000277 | 448 |
| Loss of Function | 3.18 | 5 | 20.6 | 0.243 | 9.54e-7 | 244 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000534 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Buffers cytosolic calcium. May stimulate a membrane Ca(2+)-ATPase and a 3',5'-cyclic nucleotide phosphodiesterase.;
- Pathway
- Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Metabolism of proteins;Amyloid fiber formation
(Consensus)
Recessive Scores
- pRec
- 0.601
Intolerance Scores
- loftool
- 0.279
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.469
- hipred
- Y
- hipred_score
- 0.851
- ghis
- 0.559
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Calb1
- Phenotype
- hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype;
Gene ontology
- Biological process
- short-term memory;long-term memory;locomotory behavior;retina layer formation;metanephric part of ureteric bud development;cellular protein metabolic process;regulation of cytosolic calcium ion concentration;cellular response to organic substance;metanephric collecting duct development;metanephric distal convoluted tubule development;metanephric connecting tubule development;regulation of presynaptic cytosolic calcium ion concentration;regulation of postsynaptic cytosolic calcium ion concentration;regulation of long-term synaptic potentiation
- Cellular component
- nucleus;cytosol;axon;dendrite;neuron projection;neuronal cell body;dendritic spine;calyx of Held;synapse;extracellular exosome;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;GABA-ergic synapse;presynaptic cytosol;postsynaptic cytosol
- Molecular function
- vitamin D binding;calcium ion binding;protein binding;zinc ion binding;calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration;calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration