CALB1

calbindin 1, the group of EF-hand domain containing

Basic information

Region (hg38): 8:90058607-90095475

Previous symbols: [ "CALB" ]

Links

ENSG00000104327 ∙ NCBI:793 ∙ OMIM:114050 ∙ HGNC:1434 ∙ Uniprot:P05937 ∙ 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 CALB1 gene.

• Inborn genetic diseases (3 variants)
• not provided (2 variants)

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		1
missense			3			3
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	3	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: gnomAD

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: dbNSFP

• 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