TRPM1

transient receptor potential cation channel subfamily M member 1, the group of MicroRNA protein coding host genes|Transient receptor potential cation channels

Basic information

Region (hg38): 15:31001064-31161160

Previous symbols: [ "MLSN1" ]

Links

ENSG00000134160 ∙ NCBI:4308 ∙ OMIM:603576 ∙ HGNC:7146 ∙ Uniprot:Q7Z4N2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital stationary night blindness 1C (Definitive), mode of inheritance: AR
• congenital stationary night blindness (Supportive), mode of inheritance: AD
• congenital stationary night blindness 1C (Strong), mode of inheritance: AR
• TRPM1-related retinopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Night blindness, congenital stationary, type 1C	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	19896113; 19878917; 19896109; 20300565
Dermatologic findings (eg, dry skin; a condition resembling epidermolysis bullosa simplex) have been described, but it is not clear if these are part of the core phenotype

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRPM1 gene.

• not provided (1089 variants)
• Congenital stationary night blindness 1C (162 variants)
• Inborn genetic diseases (62 variants)
• not specified (14 variants)
• Retinal dystrophy (7 variants)
• Congenital stationary night blindness (6 variants)
• TRPM1-related condition (4 variants)
• Congenital Stationary Night Blindness, Recessive (4 variants)
• Retinitis pigmentosa (2 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPM1 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			11	195	13	219
missense	1	6	505	18	18	548
nonsense	16	5	3	2	1	27
start loss		1	1		1	3
frameshift	20	3	13	5		41
inframe indel			7			7
splice donor/acceptor (+/-2bp)	2	15	1			18
splice region	2	1	25	23	2	53
non coding			19	107	69	195
Total	39	30	560	327	102

Highest pathogenic variant AF is 0.0000789

Variants in TRPM1

This is a list of pathogenic ClinVar variants found in the TRPM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-31001099-A-G		Congenital stationary night blindness 1C	Benign (Jan 13, 2018)
15-31001158-T-C		Congenital stationary night blindness 1C	Uncertain significance (Jan 12, 2018)
15-31001171-G-A		Congenital stationary night blindness 1C	Uncertain significance (Jan 12, 2018)
15-31001251-C-T		Congenital stationary night blindness 1C	Benign (Jan 12, 2018)
15-31001273-A-G		Congenital stationary night blindness 1C	Benign (Jan 13, 2018)
15-31001281-C-CT		Congenital Stationary Night Blindness, Recessive	Uncertain significance (Jun 14, 2016)
15-31001340-T-C		Congenital stationary night blindness 1C	Uncertain significance (Jan 12, 2018)
15-31001375-C-G		Congenital stationary night blindness 1C	Likely benign (Jan 12, 2018)
15-31001472-G-C		Congenital stationary night blindness 1C	Uncertain significance (Jan 12, 2018)
15-31001571-T-C		Congenital stationary night blindness 1C	Benign (Jan 19, 2019)
15-31001572-A-G		Congenital stationary night blindness 1C	Uncertain significance (Jan 12, 2018)
15-31001582-C-A		Congenital stationary night blindness 1C	Uncertain significance (Jan 13, 2018)
15-31001593-C-T		Congenital stationary night blindness 1C	Uncertain significance (Apr 27, 2017)
15-31001594-G-A		Congenital stationary night blindness 1C	Uncertain significance (Jan 13, 2018)
15-31001616-T-C		Congenital stationary night blindness 1C	Likely benign (Jan 12, 2018)
15-31001757-T-C		Congenital stationary night blindness 1C	Uncertain significance (Jan 13, 2018)
15-31001792-T-TA		Congenital Stationary Night Blindness, Recessive	Uncertain significance (Jun 14, 2016)
15-31001823-T-C			Uncertain significance (Jul 19, 2022)
15-31001831-A-C			Likely benign (Aug 24, 2023)
15-31001843-A-T			Likely benign (Apr 16, 2022)
15-31001857-TA-T		Congenital stationary night blindness 1C	Likely pathogenic (-)
15-31001861-C-CT			Likely benign (Dec 10, 2020)
15-31001862-T-A		Congenital stationary night blindness 1C	Uncertain significance (Jan 13, 2018)
15-31001868-T-A			Uncertain significance (Sep 24, 2021)
15-31001888-C-G		Congenital stationary night blindness 1C	Benign (Jan 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRPM1	protein_coding	protein_coding	ENST00000542188	27	160213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-42	0.0000398	109924	681	14678	125283	0.0633

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.131	914	903	1.01	0.0000561	10813
Missense in Polyphen		347	355.74	0.97543		4200
Synonymous	-0.981	380	356	1.07	0.0000239	3120
Loss of Function	1.03	70	80.0	0.875	0.00000457	942

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.117	0.115
Ashkenazi Jewish	0.0699	0.0690
East Asian	0.0111	0.0108
Finnish	0.0694	0.0687
European (Non-Finnish)	0.0594	0.0590
Middle Eastern	0.0111	0.0108
South Asian	0.134	0.132
Other	0.0658	0.0656

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cation channel essential for the depolarizing photoresponse of retinal ON bipolar cells. It is part of the GRM6 signaling cascade. May play a role in metastasis suppression (By similarity). May act as a spontaneously active, calcium-permeable plasma membrane channel. {ECO:0000250, ECO:0000269|PubMed:11535825, ECO:0000269|PubMed:19878917, ECO:0000269|PubMed:19896109}.
• Disease: DISEASE: Night blindness, congenital stationary, 1C (CSNB1C) [MIM:613216]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269|PubMed:19878917, ECO:0000269|PubMed:19896109, ECO:0000269|PubMed:19896113}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules;TRP channels (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.884
• rvis_EVS: 1.75
• rvis_percentile_EVS: 96.69

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.251
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.156

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trpm1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye 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 glutamate receptor signaling pathway;visual perception;retinal rod cell development;protein tetramerization;calcium ion transport into cytosol;calcium ion transmembrane transport;cellular response to light stimulus
• Cellular component: plasma membrane;integral component of plasma membrane;new growing cell tip
• Molecular function: calcium channel activity