CABP1

calcium binding protein 1, the group of EF-hand domain containing

Basic information

Region (hg38): 12:120640626-120667324

Links

ENSG00000157782

∙ NCBI:9478 ∙ OMIM:605563 ∙ HGNC:1384 ∙ Uniprot:Q9NZU7 ∙ 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 CABP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABP1 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						0
missense			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CABP1

This is a list of pathogenic ClinVar variants found in the CABP1 region.

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

Position	Phenotype	Significance	ClinVar
12-120640812-A-T	not specified	Uncertain significance (Nov 29, 2023)	2344796
12-120640959-C-T	not specified	Uncertain significance (Jul 26, 2021)	2364157
12-120641221-T-G	not specified	Uncertain significance (Jul 27, 2021)	2239511
12-120660740-A-G	not specified	Uncertain significance (May 03, 2023)	2543203
12-120660753-T-A	not specified	Uncertain significance (Oct 22, 2021)	2373226
12-120660836-G-A	not specified	Uncertain significance (Mar 24, 2023)	2529374
12-120661122-A-C	not specified	Uncertain significance (Nov 10, 2022)	2401042

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABP1	protein_coding	protein_coding	ENST00000316803	6	26773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.888	0.112	125706	0	3	125709	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.58	31	106	0.294	0.00000611	2329
Missense in Polyphen		10	59.91	0.16692		636
Synonymous	1.77	23	36.6	0.628	0.00000191	844
Loss of Function	3.23	2	15.9	0.126	0.00000147	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Modulates calcium-dependent activity of inositol 1,4,5- triphosphate receptors (ITPRs)(PubMed:14570872). Inhibits agonist- induced intracellular calcium signaling (PubMed:15980432). Enhances inactivation and does not support calcium-dependent facilitation of voltage-dependent P/Q-type calcium channels (PubMed:11865310). Causes calcium-dependent facilitation and inhibits inactivation of L-type calcium channels by binding to the same sites as calmodulin in the C-terminal domain of CACNA1C, but has an opposite effect on channel function (PubMed:15140941). Suppresses the calcium-dependent inactivation of CACNA1D (By similarity). Inhibits TRPC5 channels (PubMed:15895247). Prevents NMDA receptor-induced cellular degeneration. Required for the normal transfer of light signals through the retina (By similarity). {ECO:0000250|UniProtKB:O88751, ECO:0000250|UniProtKB:Q9JLK7, ECO:0000269|PubMed:11865310, ECO:0000269|PubMed:14570872, ECO:0000269|PubMed:15140941, ECO:0000269|PubMed:15895247, ECO:0000269|PubMed:15980432}.;

Haploinsufficiency Scores

pHI: 0.313
hipred: N
hipred_score: 0.481
ghis: 0.643

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cabp1
Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; vision/eye phenotype;

Gene ontology

Biological process: visual perception;negative regulation of protein import into nucleus;negative regulation of catalytic activity;response to stimulus
Cellular component: Golgi membrane;extracellular space;cytoskeleton;plasma membrane;cell cortex;postsynaptic density;cell junction;postsynaptic membrane;perinuclear region of cytoplasm
Molecular function: enzyme inhibitor activity;calcium ion binding;protein binding;nuclear localization sequence binding;calcium-dependent protein binding