CABP5

calcium binding protein 5, the group of EF-hand domain containing

Basic information

Region (hg38): 19:48029383-48044079

Previous symbols: [ "CABP3" ]

Links

ENSG00000105507 ∙ NCBI:56344 ∙ OMIM:607315 ∙ HGNC:13714 ∙ Uniprot:Q9NP86 ∙ 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 CABP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABP5 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in CABP5

This is a list of pathogenic ClinVar variants found in the CABP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48034217-T-G		not specified	Uncertain significance (Jun 22, 2021)
19-48034252-C-A		not specified	Uncertain significance (Jul 13, 2022)
19-48034256-C-T		not specified	Likely benign (Dec 03, 2024)
19-48034275-C-G		not specified	Uncertain significance (Feb 21, 2024)
19-48034290-G-A		not specified	Uncertain significance (Oct 25, 2022)
19-48034355-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-48039218-G-C		not specified	Uncertain significance (Jan 26, 2023)
19-48040607-T-A		not specified	Uncertain significance (Nov 13, 2024)
19-48040614-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-48040647-C-G		not specified	Uncertain significance (Feb 27, 2024)
19-48040652-G-A		not specified	Uncertain significance (Jun 28, 2024)
19-48040664-A-T		not specified	Uncertain significance (Mar 28, 2023)
19-48040677-G-C		not specified	Uncertain significance (Sep 14, 2022)
19-48040709-T-C		not specified	Uncertain significance (Nov 12, 2021)
19-48040722-C-T		not specified	Uncertain significance (Jul 26, 2021)
19-48041581-T-G		not specified	Uncertain significance (Nov 07, 2022)
19-48043861-C-T		not specified	Uncertain significance (Jul 13, 2021)
19-48043901-C-T		not specified	Uncertain significance (Nov 10, 2024)
19-48043906-C-A		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABP5	protein_coding	protein_coding	ENST00000293255	6	14101

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00479	0.891	125724	0	19	125743	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.417	93	105	0.886	0.00000648	1147
Missense in Polyphen		33	40.254	0.81978		485
Synonymous	-0.0722	37	36.4	1.02	0.00000210	319
Loss of Function	1.38	5	9.63	0.519	5.03e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000911	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.000226	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000226	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits calcium-dependent inactivation of L-type calcium channel and shifts voltage dependence of activation to more depolarized membrane potentials. Involved in the transmission of light signals (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.664
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.14

Haploinsufficiency Scores

• pHI: 0.352
• hipred: N
• hipred_score: 0.242

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cabp5

Gene ontology

• Biological process: signal transduction
• Cellular component: cytosol
• Molecular function: calcium ion binding;protein binding