CCKAR

cholecystokinin A receptor, the group of Cholecystokinin receptors

Basic information

Region (hg38): 4:26481396-26490484

Links

ENSG00000163394 ∙ NCBI:886 ∙ OMIM:118444 ∙ HGNC:1570 ∙ Uniprot:P32238 ∙ 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 CCKAR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCKAR 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in CCKAR

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

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

Position	Type	Phenotype	Significance	ClinVar
4-26481663-A-T		not specified	Uncertain significance (Nov 20, 2023)
4-26481723-C-T		not specified	Uncertain significance (Jun 05, 2023)
4-26481826-G-T		not specified	Uncertain significance (Jan 04, 2022)
4-26481832-C-T		CHOLECYSTOKININ A RECEPTOR POLYMORPHISM	Benign (-)
4-26481840-G-T		not specified	Uncertain significance (Feb 15, 2023)
4-26481891-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-26481904-C-T		not specified	Uncertain significance (Dec 02, 2022)
4-26481926-G-T		not specified	Uncertain significance (Jun 22, 2021)
4-26481931-C-T		not specified	Uncertain significance (Oct 17, 2023)
4-26481946-T-C		not specified	Uncertain significance (Jun 16, 2023)
4-26481975-A-G		not specified	Uncertain significance (May 24, 2024)
4-26482032-C-A		not specified	Uncertain significance (Jun 23, 2021)
4-26482126-C-T		not specified	Uncertain significance (Apr 27, 2022)
4-26482129-T-A		not specified	Uncertain significance (Jan 31, 2024)
4-26482129-T-C		not specified	Uncertain significance (Feb 23, 2023)
4-26483216-T-C		not specified	Uncertain significance (Oct 26, 2022)
4-26483259-G-A			Likely benign (Jul 20, 2018)
4-26483278-G-C		not specified	Uncertain significance (Nov 12, 2021)
4-26485688-G-A		not specified	Uncertain significance (Aug 01, 2022)
4-26485693-G-T		not specified	Uncertain significance (May 27, 2022)
4-26485739-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-26485814-C-G		not specified	Uncertain significance (Jan 16, 2024)
4-26485838-G-A		not specified	Uncertain significance (Jul 09, 2021)
4-26485884-C-T		not specified	Uncertain significance (Aug 08, 2023)
4-26489244-G-A		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCKAR	protein_coding	protein_coding	ENST00000295589	5	9063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00403	0.963	125654	0	94	125748	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.309	255	269	0.947	0.0000170	2805
Missense in Polyphen		107	113.55	0.94234		1191
Synonymous	-0.458	119	113	1.05	0.00000773	877
Loss of Function	1.87	6	13.4	0.449	5.65e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.000899	0.000893
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00	0.00
South Asian	0.00209	0.00209
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for cholecystokinin. Mediates pancreatic growth and enzyme secretion, smooth muscle contraction of the gall bladder and stomach. Has a 1000-fold higher affinity for CCK rather than for gastrin. It modulates feeding and dopamine-induced behavior in the central and peripheral nervous system. This receptor mediates its action by association with G proteins that activate a phosphatidylinositol-calcium second messenger system.
• Pathway: Calcium signaling pathway - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Peptide GPCRs;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.647
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.401
• hipred: Y
• hipred_score: 0.506
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.613

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cckar
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory 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); digestive/alimentary phenotype; renal/urinary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; taste/olfaction phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: neuron migration;G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;axonogenesis;feeding behavior;forebrain development;cellular response to hormone stimulus;cholecystokinin signaling pathway;regulation of hormone secretion
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: cholecystokinin receptor activity;peptide hormone binding