CABP7

calcium binding protein 7, the group of EF-hand domain containing

Basic information

Region (hg38): 22:29720003-29731833

Links

ENSG00000100314 ∙ NCBI:164633 ∙ OMIM:618759 ∙ HGNC:20834 ∙ Uniprot:Q86V35 ∙ 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 CABP7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABP7 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	14	0	0

Variants in CABP7

This is a list of pathogenic ClinVar variants found in the CABP7 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29727663-G-T		not specified	Uncertain significance (May 26, 2024)
22-29727700-A-G		not specified	Uncertain significance (Jul 20, 2022)
22-29727763-G-A		not specified	Uncertain significance (Jan 23, 2024)
22-29727790-C-T		not specified	Uncertain significance (Jul 09, 2024)
22-29727801-G-A		not specified	Uncertain significance (Apr 01, 2024)
22-29727803-A-G		not specified	Uncertain significance (Oct 17, 2023)
22-29728630-G-A		not specified	Uncertain significance (Aug 10, 2024)
22-29728696-T-A		not specified	Uncertain significance (Jan 10, 2023)
22-29728729-C-T		not specified	Uncertain significance (Oct 01, 2024)
22-29729058-G-A		not specified	Uncertain significance (Feb 03, 2022)
22-29729071-T-C		not specified	Uncertain significance (Mar 06, 2023)
22-29729074-C-T		not specified	Uncertain significance (Jun 24, 2022)
22-29729091-C-T		not specified	Uncertain significance (Jun 02, 2023)
22-29729155-C-T		not specified	Uncertain significance (Nov 24, 2024)
22-29729184-G-A		not specified	Uncertain significance (Mar 13, 2023)
22-29729452-C-A		not specified	Uncertain significance (Apr 12, 2022)
22-29729472-G-A		not specified	Uncertain significance (Dec 01, 2022)
22-29729562-T-A		not specified	Uncertain significance (Dec 05, 2022)
22-29731278-G-A		not specified	Uncertain significance (Dec 04, 2024)
22-29731314-C-A		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABP7	protein_coding	protein_coding	ENST00000216144	5	11756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.147	0.837	125720	0	13	125733	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	89	136	0.656	0.00000809	1414
Missense in Polyphen		20	32.795	0.60985		322
Synonymous	0.0771	55	55.7	0.987	0.00000358	406
Loss of Function	2.08	3	10.1	0.296	4.83e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000592	0.0000592
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000647	0.0000615
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity. {ECO:0000250}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.234
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.749
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cabp7

Gene ontology

• Cellular component: plasma membrane;integral component of membrane;trans-Golgi network membrane;perinuclear region of cytoplasm
• Molecular function: calcium ion binding