MTNR1A

melatonin receptor 1A, the group of Melatonin receptors

Basic information

Region (hg38): 4:186526792-186555567

Links

ENSG00000168412 ∙ NCBI:4543 ∙ OMIM:600665 ∙ HGNC:7463 ∙ Uniprot:P48039 ∙ 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 MTNR1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTNR1A 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				2	2	4
missense			12	1	2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	12	3	6

Variants in MTNR1A

This is a list of pathogenic ClinVar variants found in the MTNR1A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-186533547-T-C			Benign (May 13, 2021)
4-186533709-C-T		not specified	Likely benign (Jul 09, 2021)
4-186533766-C-T		not specified	Uncertain significance (Jan 31, 2024)
4-186533797-T-C			Benign (May 04, 2021)
4-186533812-T-C		not specified	Uncertain significance (Jan 23, 2024)
4-186533818-T-C			Benign (May 04, 2021)
4-186533903-C-G		not specified	Uncertain significance (Apr 13, 2022)
4-186534044-T-A		not specified	Uncertain significance (Mar 07, 2024)
4-186534107-A-G			Benign (May 05, 2021)
4-186534140-A-T		not specified	Uncertain significance (Jun 03, 2022)
4-186534154-G-A			Likely benign (Aug 09, 2018)
4-186534236-T-A		not specified	Uncertain significance (Apr 04, 2024)
4-186534268-G-A		not specified	Likely benign (Oct 14, 2023)
4-186534272-G-A			Benign (Feb 01, 2018)
4-186534300-C-T		not specified	Uncertain significance (Dec 12, 2023)
4-186534405-C-T		not specified	Uncertain significance (May 17, 2023)
4-186534468-C-T		not specified	Uncertain significance (Apr 06, 2022)
4-186534471-T-A		not specified	Uncertain significance (Jun 07, 2023)
4-186534710-AG-A			Benign (May 13, 2021)
4-186555211-A-G		not specified	Uncertain significance (Jun 29, 2022)
4-186555353-C-G		not specified	Uncertain significance (Jul 25, 2023)
4-186555360-C-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTNR1A	protein_coding	protein_coding	ENST00000307161	2	21913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.23e-7	0.161	125609	0	139	125748	0.000553

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0919	198	202	0.982	0.0000125	2267
Missense in Polyphen		34	38.324	0.88717		474
Synonymous	-0.00910	95	94.9	1.00	0.00000734	724
Loss of Function	-0.224	9	8.30	1.08	3.64e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00920	0.00847
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000379	0.000352
Middle Eastern	0.000272	0.000272
South Asian	0.0000654	0.0000653
Other	0.000704	0.000652

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: 0.136

Intolerance Scores

• loftool: 0.610
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.0846
• hipred: Y
• hipred_score: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.729

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtnr1a
• 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: G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;mating behavior;circadian rhythm
• Cellular component: plasma membrane;integral component of plasma membrane;receptor complex
• Molecular function: protein binding;melatonin receptor activity;hormone binding;organic cyclic compound binding