GeneBe

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): 15:31001065-31161160

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Night blindness, congenital stationary, type 1CARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic19896113; 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 (1127 variants)
  • Inborn_genetic_diseases (184 variants)
  • Congenital_stationary_night_blindness_1C (144 variants)
  • TRPM1-related_disorder (47 variants)
  • Retinal_dystrophy (24 variants)
  • not_specified (14 variants)
  • Congenital_stationary_night_blindness (11 variants)
  • Optic_atrophy (3 variants)
  • Hereditary_macular_dystrophy (2 variants)
  • Retinitis_pigmentosa (2 variants)
  • Congenital_Stationary_Night_Blindness,_Recessive (2 variants)
  • Cone-rod_dystrophy (1 variants)
  • Night_blindness (1 variants)
  • Intellectual_disability (1 variants)
  • Ependymoma (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. These statistics are base on transcript: NM_001252024.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
9
clinvar
276
clinvar
9
clinvar
 295
missense
27
clinvar
560
clinvar
54
clinvar
7
clinvar
 648
nonsense
21
clinvar
6
clinvar
3
clinvar
2
clinvar
 32
start loss
0
frameshift
30
clinvar
5
clinvar
9
clinvar
6
clinvar
 50
splice donor/acceptor (+/-2bp)
6
clinvar
21
clinvar
 27
Total 57 60 581 338 16

Highest pathogenic variant AF is 0.000306051

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRPM1protein_codingprotein_codingENST00000542188 27160213
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.60e-420.0000398109924681146781252830.0633
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1319149031.010.000056110813
Missense in Polyphen347355.740.975434200
Synonymous-0.9813803561.070.00002393120
Loss of Function1.037080.00.8750.00000457942

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.1170.115
Ashkenazi Jewish0.06990.0690
East Asian0.01110.0108
Finnish0.06940.0687
European (Non-Finnish)0.05940.0590
Middle Eastern0.01110.0108
South Asian0.1340.132
Other0.06580.0656

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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