CCK

cholecystokinin, the group of Neuropeptides

Basic information

Region (hg38): 3:42257824-42266185

Links

ENSG00000187094 ∙ NCBI:885 ∙ OMIM:118440 ∙ HGNC:1569 ∙ Uniprot:P06307 ∙ 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 CCK gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCK 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				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in CCK

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

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

Position	Type	Phenotype	Significance	ClinVar
3-42258162-C-T		not specified	Uncertain significance (Dec 16, 2023)
3-42263527-C-T		not specified	Likely benign (Oct 12, 2021)
3-42263617-A-G		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCK	protein_coding	protein_coding	ENST00000396169	2	8383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000330	0.210	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.653	58	73.8	0.786	0.00000400	724
Missense in Polyphen		24	29.3	0.8191		269
Synonymous	-0.00655	33	33.0	1.00	0.00000161	250
Loss of Function	-0.606	6	4.60	1.30	3.00e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000533	0.0000527
Middle Eastern	0.000111	0.000109
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This peptide hormone induces gall bladder contraction and the release of pancreatic enzymes in the gut. Its function in the brain is not clear. Binding to CCK-A receptors stimulates amylase release from the pancreas, binding to CCK-B receptors stimulates gastric acid secretion.
• Pathway: Gastric acid production;Cell-type Dependent Selectivity of CCK2R Signaling;Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.545
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.0750
• hipred: N
• hipred_score: 0.459
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cck
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system 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)

Gene ontology

• Biological process: neuron migration;release of cytochrome c from mitochondria;activation of cysteine-type endopeptidase activity involved in apoptotic process;signal transduction;G protein-coupled receptor signaling pathway;protein kinase C-activating G protein-coupled receptor signaling pathway;axonogenesis;digestion;memory;positive regulation of cell population proliferation;visual learning;regulation of signaling receptor activity;positive regulation of glutamate secretion;negative regulation of appetite;positive regulation of protein oligomerization;eating behavior;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of mitochondrial depolarization;negative regulation of eating behavior;positive regulation of sensory perception of pain;negative regulation of behavioral fear response;positive regulation of behavioral fear response
• Cellular component: extracellular region;extracellular space;axon;dendrite;axon initial segment;terminal bouton;axon hillock;perikaryon
• Molecular function: hormone activity;neuropeptide hormone activity;peptide hormone receptor binding