MC5R

melanocortin 5 receptor, the group of Melanocortin receptors

Basic information

Region (hg38): 18:13824149-13827323

Links

ENSG00000176136 ∙ NCBI:4161 ∙ OMIM:600042 ∙ HGNC:6933 ∙ Uniprot:P33032 ∙ 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 MC5R gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MC5R 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in MC5R

This is a list of pathogenic ClinVar variants found in the MC5R region.

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

Position	Type	Phenotype	Significance	ClinVar
18-13826110-C-G		not specified	Uncertain significance (Jan 30, 2024)
18-13826140-C-T			Benign (May 21, 2018)
18-13826177-G-C		not specified	Uncertain significance (Jan 04, 2024)
18-13826189-G-C		not specified	Uncertain significance (Oct 06, 2022)
18-13826228-A-G		not specified	Uncertain significance (Jun 28, 2022)
18-13826236-G-C		not specified	Uncertain significance (Nov 03, 2023)
18-13826276-A-T		not specified	Uncertain significance (Feb 27, 2024)
18-13826277-C-A		not specified	Uncertain significance (Feb 16, 2023)
18-13826277-C-T		not specified	Uncertain significance (Sep 17, 2021)
18-13826316-C-T		not specified	Uncertain significance (Sep 17, 2021)
18-13826351-G-A		not specified	Likely benign (Sep 27, 2022)
18-13826417-C-T		not specified	Uncertain significance (Jul 20, 2022)
18-13826498-G-T		not specified	Uncertain significance (Aug 21, 2023)
18-13826514-G-T		not specified	Uncertain significance (Feb 27, 2023)
18-13826571-A-G		not specified	Uncertain significance (Jan 09, 2024)
18-13826574-G-C		not specified	Uncertain significance (Sep 29, 2022)
18-13826622-G-A		not specified	Uncertain significance (Apr 04, 2024)
18-13826622-G-T		not specified	Uncertain significance (Oct 06, 2021)
18-13826648-T-C		not specified	Uncertain significance (Dec 19, 2022)
18-13826717-G-A		not specified	Uncertain significance (Mar 18, 2024)
18-13826733-G-C		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MC5R	protein_coding	protein_coding	ENST00000324750	1	2708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000651	0.298	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0722	202	205	0.986	0.0000134	2159
Missense in Polyphen		64	67.923	0.94224		811
Synonymous	-0.101	83	81.8	1.01	0.00000589	663
Loss of Function	-0.209	6	5.47	1.10	2.36e-7	70

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for MSH (alpha, beta and gamma) and ACTH. The activity of this receptor is mediated by G proteins which activate adenylate cyclase. This receptor is a possible mediator of the immunomodulation properties of melanocortins.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Peptide GPCRs;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.690
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.333
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.606

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mc5r
• Phenotype: vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-activating G protein-coupled receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: melanocortin receptor activity;protein binding;hormone binding