MCHR1

melanin concentrating hormone receptor 1, the group of Melanin concentrating hormone receptors

Basic information

Region (hg38): 22:40679272-40682812

Previous symbols: [ "GPR24" ]

Links

ENSG00000128285 ∙ NCBI:2847 ∙ OMIM:601751 ∙ HGNC:4479 ∙ Uniprot:Q99705 ∙ 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 MCHR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCHR1 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				5	1	6
missense			18	2	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	3	1	14
Total	0	0	28	10	3

Variants in MCHR1

This is a list of pathogenic ClinVar variants found in the MCHR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-40679450-C-T		not specified	Uncertain significance (Nov 09, 2023)
22-40679479-A-G		not specified	Uncertain significance (Feb 27, 2024)
22-40679500-G-A		not specified	Likely benign (Aug 15, 2023)
22-40679519-C-T		MCHR1-related disorder	Likely benign (Apr 25, 2022)
22-40679524-G-C		not specified	Uncertain significance (Jan 26, 2022)
22-40679528-A-T		MCHR1-related disorder	Benign (May 02, 2019)
22-40679531-C-G		not specified	Uncertain significance (Sep 27, 2021)
22-40679558-C-T		MCHR1-related disorder	Uncertain significance (Jan 10, 2024)
22-40679584-C-G		MCHR1-related disorder	Likely benign (Jul 13, 2022)
22-40679590-C-G		not specified	Uncertain significance (Mar 20, 2024)
22-40679591-A-C		not specified	Uncertain significance (Mar 02, 2023)
22-40679611-A-T		not specified	Uncertain significance (Jan 30, 2024)
22-40679620-C-T		not specified	Likely benign (Apr 09, 2024)
22-40679621-G-A		not specified	Uncertain significance (Mar 01, 2023)
22-40679621-G-T		not specified	Uncertain significance (Nov 29, 2023)
22-40679636-C-T		MCHR1-related disorder	Uncertain significance (Oct 26, 2023)
22-40679716-G-A		not specified	Uncertain significance (Oct 13, 2023)
22-40679729-C-T		not specified	Uncertain significance (Jul 06, 2021)
22-40680966-G-A		not specified • MCHR1-related disorder	Benign (Dec 29, 2022)
22-40681000-C-T		not specified	Uncertain significance (May 02, 2024)
22-40681007-C-T		MCHR1-related disorder	Likely benign (Apr 05, 2019)
22-40681062-G-A		MCHR1-related disorder • not specified	Uncertain significance (Jul 14, 2023)
22-40681148-G-C		MCHR1-related disorder	Likely benign (Mar 12, 2019)
22-40681173-C-T		not specified	Uncertain significance (Aug 17, 2021)
22-40681176-A-G		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCHR1	protein_coding	protein_coding	ENST00000249016	2	4065

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000474	0.671	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.749	286	253	1.13	0.0000171	2714
Missense in Polyphen		100	100.25	0.99755		1167
Synonymous	-2.36	143	111	1.28	0.00000821	925
Loss of Function	0.902	8	11.3	0.710	5.03e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000384	0.000383
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000975	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.000621	0.000621
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for melanin-concentrating hormone, coupled to both G proteins that inhibit adenylyl cyclase and G proteins that activate phosphoinositide hydrolysis. {ECO:0000269|PubMed:10421367}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);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 (i) signalling events;G alpha (q) signalling events;GPCR downstream signalling;BBSome-mediated cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.699
• rvis_EVS: 0
• rvis_percentile_EVS: 54.03

Haploinsufficiency Scores

• pHI: 0.0997
• hipred: N
• hipred_score: 0.197
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mchr1
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: generation of precursor metabolites and energy;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;neuropeptide signaling pathway;feeding behavior;positive regulation of calcium ion transport
• Cellular component: plasma membrane;integral component of plasma membrane;ciliary membrane;non-motile cilium
• Molecular function: G protein-coupled receptor activity;signaling receptor binding;protein C-terminus binding;neuropeptide receptor activity;melanin-concentrating hormone receptor activity;peptide binding;hormone binding;neuropeptide binding