TRPM1 transient receptor potential cation channel subfamily M member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRPM1provided by HGNC
Official Full Name: transient receptor potential cation channel subfamily M member 1provided by HGNC
Primary source: HGNC:HGNC:7146
See related: Ensembl:ENSG00000134160 MIM:603576; AllianceGenome:HGNC:7146
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MLSN1; CSNB1C; LTRPC1
Summary: This gene encodes a member of the transient receptor potential melastatin subfamily of transient receptor potential ion channels. The encoded protein is a calcium permeable cation channel that is expressed in melanocytes and may play a role in melanin synthesis. Specific mutations in this gene are the cause autosomal recessive complete congenital stationary night blindness-1C. The expression of this protein is inversely correlated with melanoma aggressiveness and as such it is used as a prognostic marker for melanoma metastasis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]
Expression: Biased expression in skin (RPKM 2.8) and testis (RPKM 1.1) See more
Orthologs: mouse all
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Genomic context

Location:: 15q13.3

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (31001065..31161160, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (28795157..28955270, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (31293268..31453363, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TRPM1 promotes tumor progression in acral melanoma by activating the Ca[2+]/CaMKIIdelta/AKT pathway.
Title: TRPM1 promotes tumor progression in acral melanoma by activating the Ca(2+)/CaMKIIδ/AKT pathway.
The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration.
Title: The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration.
Clinical and genetic findings in TRPM1-related congenital stationary night blindness.
Title: Clinical and genetic findings in TRPM1-related congenital stationary night blindness.
Congenital stationary night blindness in a patient with mild learning disability due to a compound heterozygous microdeletion of 15q13 and a missense mutation in TRPM1.
Title: Congenital stationary night blindness in a patient with mild learning disability due to a compound heterozygous microdeletion of 15q13 and a missense mutation in TRPM1.
Association Analysis Between Common Variants of the TRPM1 Gene and Three Mental Disorders in the Han Chinese Population.
Title: Association Analysis Between Common Variants of the TRPM1 Gene and Three Mental Disorders in the Han Chinese Population.
Serum SUR1 and TRPM4 in patients with subarachnoid hemorrhage.
Title: Serum SUR1 and TRPM4 in patients with subarachnoid hemorrhage.
Genetic polymorphisms of transient receptor potential melastatin 1 correlate with voriconazole-related visual adverse events.
Title: Genetic polymorphisms of transient receptor potential melastatin 1 correlate with voriconazole-related visual adverse events.
TRPM1 Mutations are the Most Common Cause of Autosomal Recessive Congenital Stationary Night Blindness (CSNB) in the Palestinian and Israeli Populations.
Title: TRPM1 Mutations are the Most Common Cause of Autosomal Recessive Congenital Stationary Night Blindness (CSNB) in the Palestinian and Israeli Populations.
A case of melanoma-associated retinopathy with autoantibodies against TRPM1.
Title: A case of melanoma-associated retinopathy with autoantibodies against TRPM1.
A novel homozygous c.1394T>A (p.Met465Lys) missense mutation in TRPM1 was identified in two siblings.
Title: Long-term follow-up of retinal function and structure in TRPM1-associated complete congenital stationary night blindness.

Submit: New GeneRIF Correction See all GeneRIFs (42)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital stationary night blindness 1C MedGen: C2750747 OMIM: 613216 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide pharmacogenomic analysis of response to treatment with antipsychotics. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-N21111 (e-PCR)
- UniSTS:47108

STS-N33330 (e-PCR)
- UniSTS:77877

SHGC-83514 (e-PCR)
- UniSTS:101729

STS-N30022 (e-PCR)
- UniSTS:57729

SHGC-31211 (e-PCR)
- UniSTS:58286

D15S1124 (e-PCR)
- UniSTS:154545

RH98791 (e-PCR)
- UniSTS:83904

STS-N35472 (e-PCR)
- UniSTS:36318

RH69308 (e-PCR)
- UniSTS:27130

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables calcium channel activity	TAS Traceable Author Statement more info
enables monoatomic cation transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in G protein-coupled glutamate receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium ion import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium ion transmembrane transport	TAS Traceable Author Statement more info
involved_in cellular response to light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in metal ion transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic cation transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic cation transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in protein tetramerization	IEA Inferred from Electronic Annotation more info
involved_in visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: transient receptor potential cation channel subfamily M member 1

Names: TRPM1-203 APA Isoform, Intron 10; TRPM1-203 APA Isoform, Intron 3; long transient receptor potential channel 1; melastatin-1; transient receptor potential melastatin family

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_016453.2 RefSeqGene

Range

64549..165209

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001252020.2 → NP_001238949.1 transient receptor potential cation channel subfamily M member 1 isoform 1

See identical proteins and their annotated locations for NP_001238949.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

BU743036, HM135791

Consensus CDS

CCDS58347.1

UniProtKB/TrEMBL

A0A0G2JN34

Related

ENSP00000452946.2, ENST00000558445.6

Conserved Domains (2) summary

pfam00520
Location:893 → 1123

Ion_trans; Ion transport protein

pfam16519
Location:1222 → 1273

TRPM_tetra; Tetramerization domain of TRPM
NM_001252024.2 → NP_001238953.1 transient receptor potential cation channel subfamily M member 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate exon in the 5' coding region. These differences cause translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AC009562, BC058286, BU743036, HM135790

Consensus CDS

CCDS58346.1

UniProtKB/TrEMBL

A0A0G2JMR4

Related

ENSP00000256552.7, ENST00000256552.11

Conserved Domains (2) summary

pfam00520
Location:876 → 1106

Ion_trans; Ion transport protein

pfam16519
Location:1205 → 1256

TRPM_tetra; Tetramerization domain of TRPM
NM_001252030.2 → NP_001238959.1 transient receptor potential cation channel subfamily M member 1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, 3' UTR, and coding region, compared to variant 1. The resulting isoform (4) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC009562, BC058286, BU741333

Consensus CDS

CCDS58345.1

UniProtKB/Swiss-Prot

Q7Z4N2

Related

ENSP00000453851.1, ENST00000559179.2
NM_002420.6 → NP_002411.3 transient receptor potential cation channel subfamily M member 1 isoform 2

See identical proteins and their annotated locations for NP_002411.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC009562, AF071787, BU743036, BU933033, HM135791

Consensus CDS

CCDS10024.2

UniProtKB/Swiss-Prot

D9IDV2, D9IDV3, F8W865, H0YN37, O75560, Q6PE48, Q7Z4N1, Q7Z4N2, Q7Z4N3, Q7Z4N4, Q7Z4N5

UniProtKB/TrEMBL

A0A0G2JMJ5

Related

ENSP00000380897.2, ENST00000397795.7

Conserved Domains (2) summary

pfam00520
Location:854 → 1084

Ion_trans; Ion transport protein

pfam16519
Location:1183 → 1234

TRPM_tetra; Tetramerization domain of TRPM

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

31001065..31161160 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

NW_011332701.1 Reference GRCh38.p14 PATCHES

Range

3174373..3334472 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331796.1 → XP_054187771.1 transient receptor potential cation channel subfamily M member 1 isoform X1
XM_054331797.1 → XP_054187772.1 transient receptor potential cation channel subfamily M member 1 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

3286825..3446924 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330024.1 → XP_054185999.1 transient receptor potential cation channel subfamily M member 1 isoform X1
XM_054330025.1 → XP_054186000.1 transient receptor potential cation channel subfamily M member 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

28795157..28955270 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054377959.1 → XP_054233934.1 transient receptor potential cation channel subfamily M member 1 isoform X3
XM_054377960.1 → XP_054233935.1 transient receptor potential cation channel subfamily M member 1 isoform X4