CALB2

calbindin 2, the group of EF-hand domain containing

Basic information

Region (hg38): 16:71358713-71390436

Links

ENSG00000172137 ∙ NCBI:794 ∙ OMIM:114051 ∙ HGNC:1435 ∙ Uniprot:P22676 ∙ 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 CALB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALB2 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			15			15
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	15	1	0

Variants in CALB2

This is a list of pathogenic ClinVar variants found in the CALB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-71372177-A-G		not specified	Uncertain significance (Jul 20, 2022)
16-71377688-G-C		not specified	Uncertain significance (Jun 29, 2023)
16-71377693-G-C		not specified	Uncertain significance (May 23, 2023)
16-71382762-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-71383379-G-C		not specified	Uncertain significance (Jul 08, 2022)
16-71383386-T-C		not specified	Uncertain significance (Jul 17, 2023)
16-71383404-C-G		not specified	Uncertain significance (Jan 02, 2024)
16-71383443-T-C		not specified	Uncertain significance (Aug 05, 2024)
16-71383991-G-A		not specified	Uncertain significance (Mar 06, 2023)
16-71384353-A-G		not specified	Uncertain significance (Oct 04, 2022)
16-71384355-G-A		not specified	Uncertain significance (Nov 21, 2023)
16-71384784-G-A		not specified	Uncertain significance (May 18, 2023)
16-71385579-T-C		not specified	Likely benign (Jul 25, 2023)
16-71385585-C-T		not specified	Likely benign (Dec 11, 2023)
16-71385593-T-C		not specified	Uncertain significance (Apr 05, 2023)
16-71389788-G-A		not specified	Uncertain significance (Jan 12, 2024)
16-71389798-T-C		not specified	Uncertain significance (Aug 22, 2023)
16-71389821-C-T		not specified	Uncertain significance (Oct 06, 2024)
16-71389837-T-C		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALB2	protein_coding	protein_coding	ENST00000302628	11	31726

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.54e-7	0.845	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.201	151	158	0.955	0.00000891	1812
Missense in Polyphen		37	43.618	0.84828		522
Synonymous	-1.43	82	67.1	1.22	0.00000462	452
Loss of Function	1.50	13	20.3	0.641	9.47e-7	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000276
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calretinin is a calcium-binding protein which is abundant in auditory neurons.

Intolerance Scores

• loftool: 0.395
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.329
• hipred: N
• hipred_score: 0.377
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calb2
• Phenotype: normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: regulation of cytosolic calcium ion concentration;regulation of presynaptic cytosolic calcium ion concentration;regulation of long-term synaptic potentiation
• Cellular component: nucleus;cytosol;gap junction;dendrite;neuron projection;synapse;synaptic membrane;parallel fiber to Purkinje cell synapse;presynapse
• Molecular function: calcium ion binding;calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration