Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	4308
Gene name Gene Name - the full gene name approved by the HGNC.	Transient receptor potential cation channel subfamily M member 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TRPM1
Synonyms (NCBI Gene) Gene synonyms aliases	CSNB1C, LTRPC1, MLSN1
Chromosome Chromosome number	15
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	15q13.3
Summary Summary of gene provided in NCBI Entrez Gene.	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 syn

Show/Hide all(15)

SNP ID	Visualize variation	Clinical significance	Consequence
rs138886378	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, genic downstream transcript variant
rs150441866	A>C	Likely-pathogenic	Stop gained, coding sequence variant, intron variant
rs191205969	A>G	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant
rs267607139	G>T	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs267607141	G>A	Pathogenic	Coding sequence variant, stop gained
rs372529012	A>C,G	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, synonymous variant, stop gained
rs387906862	G>A	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs763546583	G>A	Pathogenic	Genic downstream transcript variant, stop gained, coding sequence variant
rs768701595	C>T	Likely-pathogenic, uncertain-significance	Genic downstream transcript variant, synonymous variant, coding sequence variant
rs770561064	C>T	Likely-pathogenic	Initiator codon variant, missense variant, coding sequence variant
rs772011426	TTAC>-	Pathogenic	Intron variant, splice donor variant, genic downstream transcript variant
rs1555424166	C>T	Likely-pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant
rs1555424849	C>T	Likely-pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant
rs1596017653	A>T	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs1596029830	T>A	Pathogenic	Coding sequence variant, genic downstream transcript variant, stop gained

Show/Hide all(48)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029939	hsa-miR-26b-5p	Microarray	19088304
MIRT515354	hsa-miR-4438	PAR-CLIP	23446348
MIRT515355	hsa-miR-6889-3p	PAR-CLIP	23446348
MIRT515353	hsa-miR-4252	PAR-CLIP	23446348
MIRT515352	hsa-miR-5095	PAR-CLIP	23446348
MIRT515351	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT515350	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT515349	hsa-miR-619-5p	PAR-CLIP	23446348
MIRT515354	hsa-miR-4438	PAR-CLIP	23446348
MIRT515355	hsa-miR-6889-3p	PAR-CLIP	23446348
MIRT515353	hsa-miR-4252	PAR-CLIP	23446348
MIRT515352	hsa-miR-5095	PAR-CLIP	23446348
MIRT515351	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT515350	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT515349	hsa-miR-619-5p	PAR-CLIP	23446348
MIRT1457294	hsa-miR-1273f	CLIP-seq
MIRT1457295	hsa-miR-34c-3p	CLIP-seq
MIRT1457296	hsa-miR-4423-5p	CLIP-seq
MIRT1457297	hsa-miR-4781-3p	CLIP-seq
MIRT2137122	hsa-miR-4427	CLIP-seq
MIRT2137123	hsa-miR-4680-3p	CLIP-seq
MIRT2357918	hsa-miR-106a	CLIP-seq
MIRT2357919	hsa-miR-106b	CLIP-seq
MIRT2357920	hsa-miR-150	CLIP-seq
MIRT2357921	hsa-miR-17	CLIP-seq
MIRT2357922	hsa-miR-20a	CLIP-seq
MIRT2357923	hsa-miR-20b	CLIP-seq
MIRT2357924	hsa-miR-302a	CLIP-seq
MIRT2357925	hsa-miR-302b	CLIP-seq
MIRT2357926	hsa-miR-302c	CLIP-seq
MIRT2357927	hsa-miR-302d	CLIP-seq
MIRT2357928	hsa-miR-302e	CLIP-seq
MIRT2357929	hsa-miR-3159	CLIP-seq
MIRT2357930	hsa-miR-372	CLIP-seq
MIRT2357931	hsa-miR-373	CLIP-seq
MIRT2357932	hsa-miR-4282	CLIP-seq
MIRT2137122	hsa-miR-4427	CLIP-seq
MIRT2137123	hsa-miR-4680-3p	CLIP-seq
MIRT2357933	hsa-miR-4757-5p	CLIP-seq
MIRT2357934	hsa-miR-519d	CLIP-seq
MIRT2357935	hsa-miR-520a-3p	CLIP-seq
MIRT2357936	hsa-miR-520b	CLIP-seq
MIRT2357937	hsa-miR-520c-3p	CLIP-seq
MIRT2357938	hsa-miR-520d-3p	CLIP-seq
MIRT2357939	hsa-miR-520e	CLIP-seq
MIRT2357940	hsa-miR-520g	CLIP-seq
MIRT2357941	hsa-miR-520h	CLIP-seq
MIRT2357942	hsa-miR-93	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
MITF	Activation	14744763;15577322
MITF	Unknown	20482673

Show/Hide all(31)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005216	Function	Monoatomic ion channel activity	IEA
GO:0005261	Function	Monoatomic cation channel activity	IEA
GO:0005262	Function	Calcium channel activity	IBA
GO:0005262	Function	Calcium channel activity	IDA	23452348
GO:0005262	Function	Calcium channel activity	TAS	9806836
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005783	Component	Endoplasmic reticulum	IDA	30027108
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	9806836
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006816	Process	Calcium ion transport	IBA
GO:0007216	Process	G protein-coupled glutamate receptor signaling pathway	IMP	23452348
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IMP	19878917
GO:0008324	Function	Monoatomic cation transmembrane transporter activity	IDA	21278253
GO:0016020	Component	Membrane	IEA
GO:0030424	Component	Axon	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0042995	Component	Cell projection	IEA
GO:0046873	Function	Metal ion transmembrane transporter activity	IEA
GO:0051262	Process	Protein tetramerization	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0070588	Process	Calcium ion transmembrane transport	IEA
GO:0070588	Process	Calcium ion transmembrane transport	TAS
GO:0071482	Process	Cellular response to light stimulus	IMP	19896109
GO:0098655	Process	Monoatomic cation transmembrane transport	IBA
GO:0098655	Process	Monoatomic cation transmembrane transport	IDA	21278253
GO:0098703	Process	Calcium ion import across plasma membrane	IDA	23452348

MIM	HGNC	e!Ensembl
603576	7146	ENSG00000134160

Protein

UniProt ID

Q7Z4N2

Protein name

Transient receptor potential cation channel subfamily M member 1 (Long transient receptor potential channel 1) (LTrpC1) (Melastatin-1)

Protein function

Constitutively open nonselective divalent cation-conducting channels which mediate the influx of Ca(2+), Mg(2+), Mn(2+), Ba(2+), and Ni(2+) into the cytoplasm, leading to membrane depolarization (PubMed:11535825, PubMed:19436059, PubMed:21278253

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF18139	LSDAT_euk	70 → 335	SLOG in TRPM	Family
PF00520	Ion_trans	828 → 1087	Ion transport protein	Family
PF16519	TRPM_tetra	1179 → 1234	Tetramerisation domain of TRPM	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in the retina where it localizes to the outer plexiform layer. Specifically, it is expressed in retinal bipolar cells (BPCs) of the ON subtype (PubMed:30027108). Highly expressed in benign melanocytic nevi and diffusely expre

Sequence

MKDSNRCCCGQFTNQHIPPLPSATPSKNEEESKQVETQPEKWSVAKHTQSYPTDSYGVLE
FQGGGYSNKAMYIRVSYDTKPDSLLHLMVKDWQLELPKLLISVHGGLQNFEMQPKLKQVF
GKGLIKAAMTTGAWIFTGGVSTGVISHVGDALKDHSSKSRGRVCAIGIAPWGIVENKEDL
VGKDVTRVYQTMSNPLSKLSVLNNSHTHFILADNGTLGKYGAEVKLRRLLEKHISLQKIN
TRLGQGVPLVGLVVEGGPNVVSIVLEYLQEEPPIPVVICDGSGRASDILSFAHKYCEEGG
IINESLREQLLVTIQKTFNYNKAQSHQLFAIIMECMKKKELVTVFRMGSEGQQDIEMAIL
TALLKGTNVSAPDQLSLALAWNRVDIARSQIFVFGPHWPPLGSLAPPTDSKATEKEKKPP
MATTKGGRGKGKGKKKGKVKEEVEEETDPRKIELLNWVNALEQAMLDALVLDRVDFVKLL
IENGVNMQHFLTIPRLEELYNTRLGPPNTLHLLVRDVKKSNLPPDYHISLIDIGLVLEYL
MGGAYRCNYTRKNFRTLYNNLFGPKRPKALKLLGMEDDEPPAKGKKKKKKKKEEEIDIDV
DDPAVSRFQYPFHELMVWAVLMKRQKMAVFLWQRGEESMAKALVACKLYKAMAHESSESD
LVDDISQDLDNNSKDFGQLALELLDQSYKHDEQIAMKLLTYELKNWSNSTCLKLAVAAKH
RDFIAHTCSQMLLTDMWMGRLRMRKNPGLKVIMGILLPPTILFLEFRTYDDFSYQTSKEN
EDGKEKEEENTDANADAGSRKGDEENEHKKQRSIPIGTKICEFYNAPIVKFWFYTISYLG
YLLLFNYVILVRMDGWPSLQEWIVISYIVSLALEKIREILMSEPGKLSQKIKVWLQEYWN
ITDLVAISTFMIGAILRLQNQPYMGYGRVIYCVDIIFWYIRVLDIFGVNKYLGPYVMMIG
KMMIDMLYFVVIMLVVLMSFGVARQAILHPEEKPSWKLARNIFYMPYWMIYGEVFADQID
LYAMEINPPCGENLYDEEGKRLPPCIPGAWLTPALMACYLLVANILLVNLLIAVFNNTFF
EVKSISNQVWKFQRYQLIMTFHDRPVLPPPMIILSHIYIIIMRLSGRCRKKREGDQEERD
RGLKLFLSDEELKRLHEFEEQCVQEHFREKEDEQQSSSDERIRVTSERVENMSMRLEEIN
ERETFMKTSLQTVDLRLAQLEELSNRMVNALENLAGIDRSDLIQARSRASSECEATYLLR
QSSINSADGYSLYRYHFNGEELLFEDTSLSTSPGTGVRKKTCSFRIKEEKDVKTHLVPEC
QNSLHLSLGTSTSATPDGSHLAVDDLKNAEESKLGPDIGISKEDDERQTDSKKEETISPS
LNKTDVIHGQDKSDVQNTQLTVETTNIEGTISYPLEETKITRYFPDETINACKTMKSRSF
VYSRGRKLVGGVNQDVEYSSITDQQLTTEWQCQVQKITRSHSTDIPYIVSEAAVQAEHKE
QFADMQDEHHVAEAIPRIPRLSLTITDRNGMENLLSVKPDQTLGFPSLRSKSLHGHPRNV
KSIQGKLDRSGHASSVSSLVIVSGMTAEEKKVKKEKASTETEC

Sequence length

1603

Interactions

View interactions

	Reactome
			TRP channels

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Congenital stationary night blindness	Congenital stationary night blindness 1C, congenital stationary night blindness	rs387906862, rs372529012, rs786205113, rs1485132228, rs772011426, rs778390089, rs150441866, rs869312176, rs779821510, rs770380556, rs763546583, rs748046539, rs765645888, rs1555418784, rs766862238 View all (7 more)	N/A
retinal dystrophy	Retinal dystrophy	rs2034398158, rs2034427266, rs760391688	N/A

Show/Hide Unknown Diseases (6)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Diabetes	Type 2 diabetes	N/A	N/A	GWAS
Ependymoma	ependymoma	N/A	N/A	ClinVar
Huntington Disease	Huntington's disease progression	N/A	N/A	GWAS
Myasthenia Gravis	Myasthenia gravis	N/A	N/A	GWAS
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
Retinitis Pigmentosa	retinitis pigmentosa	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Albuminuria	Associate	21439949
Atrial Fibrillation	Stimulate	28839241
Autistic Disorder	Associate	23375656
Bipolar Disorder	Associate	19878917
Cataract	Associate	37511188
Cognitive Dysfunction	Associate	37107586
Drug Related Side Effects and Adverse Reactions	Associate	30194076
Fetal Alcohol Spectrum Disorders	Associate	35633130
Glioblastoma	Associate	34238116
Horse Diseases	Associate	19896113
Hypertensive Retinopathy	Associate	35633130
Macular Degeneration	Associate	28813576, 31995762
Melanoma	Inhibit	19396153, 20482673
Melanoma	Associate	22897572, 35181301
Melanoma Cutaneous Malignant	Associate	19396153, 22897572
Myopia	Associate	31908403, 34064005
Neoplasm Metastasis	Inhibit	19587221
Neoplasm Metastasis	Associate	21072171
Neoplasms	Inhibit	21072171
Nevus Epithelioid and Spindle Cell	Associate	19396153
Nevus Pigmented	Associate	20482673
Night blindness congenital stationary	Associate	19878917, 19896109, 19896113, 23452348, 24715752, 29522070, 31427709, 31908403, 34064005, 35633130, 35872165, 36499293
Nystagmus Pathologic	Associate	31908403, 34064005
Pigmentation Disorders	Associate	35181301
Poroma	Associate	19396153
Retinal Degeneration	Associate	31908403

TRPM1 (transient receptor potential cation channel subfamily M member 1)