MTNR1B

melatonin receptor 1B, the group of Melatonin receptors

Basic information

Region (hg38): 11:92969650-92985066

Links

ENSG00000134640 ∙ NCBI:4544 ∙ OMIM:600804 ∙ HGNC:7464 ∙ Uniprot:P49286 ∙ 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 MTNR1B gene.

• Inborn genetic diseases (9 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTNR1B 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	2
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in MTNR1B

This is a list of pathogenic ClinVar variants found in the MTNR1B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-92969757-G-A		not specified	Uncertain significance (Nov 17, 2022)
11-92969759-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-92969796-G-A		MTNR1B-related disorder	Benign (Oct 24, 2019)
11-92969811-G-A		not specified	Likely benign (Dec 22, 2023)
11-92969849-G-C		Diabetes mellitus type 2, susceptibility to	risk factor (Jan 29, 2012)
11-92969904-T-G		Diabetes mellitus type 2, susceptibility to	risk factor (Jan 29, 2012)
11-92981507-C-T		Diabetes mellitus type 2, susceptibility to	risk factor (Jan 29, 2012)
11-92981536-G-A		not specified	Uncertain significance (Nov 17, 2023)
11-92981559-C-T		MTNR1B-related disorder	Likely benign (May 01, 2019)
11-92981572-G-A		not specified	Uncertain significance (Feb 10, 2022)
11-92981601-C-T			Benign (Apr 10, 2018)
11-92981625-C-G		not specified	Uncertain significance (Jan 16, 2024)
11-92981645-A-G		not specified	Uncertain significance (Sep 27, 2021)
11-92981681-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-92981727-C-T		MTNR1B-related disorder	Likely benign (Mar 04, 2019)
11-92981759-G-T		not specified	Uncertain significance (Sep 16, 2021)
11-92981769-G-T		not specified	Uncertain significance (Mar 06, 2023)
11-92981816-C-A		MTNR1B-related disorder	Likely benign (Feb 14, 2020)
11-92981824-A-G		not specified	Uncertain significance (Mar 04, 2024)
11-92981866-G-T		not specified	Uncertain significance (Mar 29, 2023)
11-92981951-A-G		MTNR1B-related disorder	Benign (Nov 06, 2019)
11-92981969-G-T		not specified	Uncertain significance (Oct 16, 2023)
11-92981990-T-C		not specified	Uncertain significance (May 15, 2023)
11-92982039-C-T		MTNR1B-related disorder	Likely benign (May 28, 2019)
11-92982055-C-G		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTNR1B	protein_coding	protein_coding	ENST00000257068	2	15347

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000648	0.752	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.454	233	214	1.09	0.0000127	2332
Missense in Polyphen		54	53.221	1.0146		675
Synonymous	-2.04	119	93.9	1.27	0.00000570	777
Loss of Function	0.962	6	9.14	0.657	4.83e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000166	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High affinity receptor for melatonin. Likely to mediate the reproductive and circadian actions of melatonin. The activity of this receptor is mediated by pertussis toxin sensitive G proteins that inhibit adenylate cyclase activity.
• Pathway: Circadian entrainment - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Small Ligand GPCRs;Melatonin metabolism and effects;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.356
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• pHI: 0.113
• hipred: Y
• hipred_score: 0.502
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtnr1b
• Phenotype: normal phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;chemical synaptic transmission;negative regulation of cGMP-mediated signaling;glucose homeostasis;camera-type eye development;negative regulation of neuron apoptotic process;positive regulation of circadian sleep/wake cycle, non-REM sleep;negative regulation of insulin secretion;regulation of insulin secretion;negative regulation of cytosolic calcium ion concentration;negative regulation of transmission of nerve impulse;positive regulation of transmission of nerve impulse;positive regulation of blood vessel diameter;regulation of neuronal action potential;negative regulation of delayed rectifier potassium channel activity
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;protein binding;melatonin receptor activity