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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	57192
Gene name	Mucolipin TRP cation channel 1
Gene symbol	MCOLN1
Synonyms (NCBI Gene)	LECDMG-2ML1ML4MLIVMST080MSTP080TRP-ML1TRPM-L1TRPML1
Chromosome	19
Chromosome location	19p13.2
Summary	This gene encodes a memberof the transient receptor potential (TRP) cation channel gene family. The transmembrane protein localizes to intracellular vesicular membranes including lysosomes, and functions in the late endocytic pathway and in the regulation

Show/Hide all (32)

SNP ID	Visualize variation	Clinical significance	Consequence
rs73003348	C>T	Benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs121908371	C>T	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, stop gained
rs121908372	G>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs121908374	C>T	Pathogenic	Coding sequence variant, missense variant
rs200484869	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs201232288	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs376777270	C>G,T	Likely-benign, likely-pathogenic	Synonymous variant, coding sequence variant, stop gained
rs566285864	C>G,T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs754097561	G>A,T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs755042147	T>-	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant
rs767122713	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs767950930	G>A	Pathogenic-likely-pathogenic	Splice donor variant
rs779141908	CTGCTGCAGAACGTGAGGCTTC>-	Likely-pathogenic	Splice donor variant, intron variant, coding sequence variant
rs797044817	TTC>-	Pathogenic	Coding sequence variant, inframe deletion
rs797044818	A>G	Pathogenic	Missense variant, coding sequence variant
rs797044822	->T	Pathogenic	Frameshift variant, coding sequence variant
rs797044823	->GGCCGCAGCAG	Pathogenic	Frameshift variant, coding sequence variant
rs797044827	T>C	Pathogenic	Missense variant, coding sequence variant
rs797044828	C>G	Pathogenic	Missense variant, coding sequence variant
rs797044829	G>A	Pathogenic	Missense variant, coding sequence variant
rs886041533	->C	Pathogenic	Frameshift variant, coding sequence variant
rs1057516458	G>A,C	Likely-pathogenic	Splice acceptor variant
rs1057516531	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs1057516904	->A	Pathogenic, likely-pathogenic	Coding sequence variant, frameshift variant
rs1057517040	->A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057517335	A>G	Likely-pathogenic	Splice acceptor variant
rs1057517453	A>G	Likely-pathogenic	Splice acceptor variant
rs1057518781	G>A,C	Likely-pathogenic	Splice donor variant
rs1555742120	ACGG>-	Pathogenic	Frameshift variant, coding sequence variant
rs1555742162	T>C	Likely-pathogenic	Splice donor variant
rs1599254152	G>A	Pathogenic	Splice donor variant
rs1599255682	C>G	Likely-pathogenic	Coding sequence variant, stop gained

Show/Hide all (29)

miRTarBase ID	miRNA	Experiments
MIRT2568446	hsa-miR-1283	CLIP-seq
MIRT2568447	hsa-miR-3178	CLIP-seq
MIRT2568448	hsa-miR-3180	CLIP-seq
MIRT2568449	hsa-miR-3180-3p	CLIP-seq
MIRT2568450	hsa-miR-3196	CLIP-seq
MIRT2568451	hsa-miR-4270	CLIP-seq
MIRT2568452	hsa-miR-4290	CLIP-seq
MIRT2568453	hsa-miR-4441	CLIP-seq
MIRT2568454	hsa-miR-4488	CLIP-seq
MIRT2568455	hsa-miR-4537	CLIP-seq
MIRT2568456	hsa-miR-4634	CLIP-seq
MIRT2568457	hsa-miR-4645-5p	CLIP-seq
MIRT2568458	hsa-miR-4667-3p	CLIP-seq
MIRT2568459	hsa-miR-4673	CLIP-seq
MIRT2568460	hsa-miR-4697-5p	CLIP-seq
MIRT2568461	hsa-miR-4750	CLIP-seq
MIRT2568462	hsa-miR-4781-5p	CLIP-seq
MIRT2568463	hsa-miR-4787-5p	CLIP-seq
MIRT2568446	hsa-miR-1283	CLIP-seq
MIRT2568447	hsa-miR-3178	CLIP-seq
MIRT2568451	hsa-miR-4270	CLIP-seq
MIRT2568452	hsa-miR-4290	CLIP-seq
MIRT2568453	hsa-miR-4441	CLIP-seq
MIRT2568455	hsa-miR-4537	CLIP-seq
MIRT2568456	hsa-miR-4634	CLIP-seq
MIRT2568457	hsa-miR-4645-5p	CLIP-seq
MIRT2568458	hsa-miR-4667-3p	CLIP-seq
MIRT2568459	hsa-miR-4673	CLIP-seq
MIRT2568461	hsa-miR-4750	CLIP-seq

Show/Hide all (81)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001891	Component	Phagocytic cup	IEA
GO:0002250	Process	Adaptive immune response	IEA
GO:0002376	Process	Immune system process	IEA
GO:0005253	Function	Monoatomic anion channel activity	IEA
GO:0005253	Function	Monoatomic anion channel activity	ISS
GO:0005261	Function	Monoatomic cation channel activity	IEA
GO:0005261	Function	Monoatomic cation channel activity	NAS	11030752
GO:0005262	Function	Calcium channel activity	IDA	25720963, 29019983
GO:0005262	Function	Calcium channel activity	IEA
GO:0005262	Function	Calcium channel activity	TAS
GO:0005267	Function	Potassium channel activity	IEA
GO:0005267	Function	Potassium channel activity	ISS
GO:0005272	Function	Sodium channel activity	IEA
GO:0005272	Function	Sodium channel activity	ISS
GO:0005381	Function	Iron ion transmembrane transporter activity	IDA	18794901
GO:0005381	Function	Iron ion transmembrane transporter activity	IEA
GO:0005381	Function	Iron ion transmembrane transporter activity	TAS
GO:0005515	Function	Protein binding	IPI	21224396, 25130899, 32296183
GO:0005654	Component	Nucleoplasm	IDA
GO:0005764	Component	Lysosome	IDA	21224396
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	HDA	17897319
GO:0005765	Component	Lysosomal membrane	IBA
GO:0005765	Component	Lysosomal membrane	IDA	25720963
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IEA
GO:0005770	Component	Late endosome	IDA	21224396
GO:0005794	Component	Golgi apparatus	IDA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	NAS	11013137
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006812	Process	Monoatomic cation transport	NAS	11030752
GO:0006816	Process	Calcium ion transport	IEA
GO:0007040	Process	Lysosome organization	IDA	32753672, 35662396
GO:0008289	Function	Lipid binding	IEA
GO:0010008	Component	Endosome membrane	TAS
GO:0016020	Component	Membrane	IDA	29019983
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	11030752
GO:0019722	Process	Calcium-mediated signaling	IEA
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0030670	Component	Phagocytic vesicle membrane	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031902	Component	Late endosome membrane	IEA
GO:0033572	Process	Transferrin transport	TAS
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0034755	Process	Iron ion transmembrane transport	IEA
GO:0034755	Process	Iron ion transmembrane transport	IMP	18794901
GO:0035725	Process	Sodium ion transmembrane transport	IEA
GO:0042802	Function	Identical protein binding	IPI	29019983, 30305615
GO:0042995	Component	Cell projection	IEA
GO:0043235	Component	Receptor complex	IDA	23382219
GO:0045824	Process	Negative regulation of innate immune response	IDA	35662396
GO:0051209	Process	Release of sequestered calcium ion into cytosol	IEA
GO:0051289	Process	Protein homotetramerization	IDA	29019983
GO:0051289	Process	Protein homotetramerization	IEA
GO:0070588	Process	Calcium ion transmembrane transport	IDA	29019983
GO:0070588	Process	Calcium ion transmembrane transport	TAS
GO:0071277	Process	Cellular response to calcium ion	IEA
GO:0071277	Process	Cellular response to calcium ion	ISS
GO:0071467	Process	Cellular response to pH	IEA
GO:0071467	Process	Cellular response to pH	ISS
GO:0071805	Process	Potassium ion transmembrane transport	IEA
GO:0072345	Function	NAADP-sensitive calcium-release channel activity	IBA
GO:0072345	Function	NAADP-sensitive calcium-release channel activity	IEA
GO:0090382	Process	Phagosome maturation	IDA	27623384
GO:0090382	Process	Phagosome maturation	IEA
GO:0097352	Process	Autophagosome maturation	IEA
GO:0097682	Function	Intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity	IEA
GO:0097682	Function	Intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity	ISS
GO:0098655	Process	Monoatomic cation transmembrane transport	IEA
GO:0098656	Process	Monoatomic anion transmembrane transport	IEA
GO:0099604	Function	Ligand-gated calcium channel activity	IDA	25720963, 29019983
GO:0140367	Process	Antibacterial innate immune response	IDA	32753672, 35662396
GO:1900181	Process	Negative regulation of protein localization to nucleus	IDA	35662396
GO:1900182	Process	Positive regulation of protein localization to nucleus	IDA	25720963, 32753672
GO:1901660	Process	Calcium ion export	IDA	25720963
GO:1905673	Process	Positive regulation of lysosome organization	IDA	32753672
GO:1905673	Process	Positive regulation of lysosome organization	IDA	25720963

MIM	HGNC	e!Ensembl
605248	13356	ENSG00000090674

Q9GZU1

Protein name

Mucolipin-1 (ML1) (MG-2) (Mucolipidin) (Transient receptor potential channel mucolipin 1) (TRPML1)

Protein function

Nonselective cation channel probably playing a role in the regulation of membrane trafficking events and of metal homeostasis (PubMed:11013137, PubMed:12459486, PubMed:14749347, PubMed:15336987, PubMed:18794901, PubMed:25720963, PubMed:27623384,

PDB

5TJA , 5TJB , 5TJC , 5WJ5 , 5WJ9 , 6E7P , 6E7Y , 6E7Z , 7MGL

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08016	PKD_channel	378 → 524	Polycystin cation channel	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed in adult and fetal tissues. {ECO:0000269|PubMed:10973263, ECO:0000269|PubMed:11013137, ECO:0000269|PubMed:11030752}.

Sequence

MTAPAGPRGSETERLLTPNPGYGTQAGPSPAPPTPPEEEDLRRRLKYFFMSPCDKFRAKG
RKPCKLMLQVVKILVVTVQLILFGLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAY
TREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPAND
TFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTI
NLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSFRLL
FDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFMWRQRGRVISLWERLEFVNGWYILLVT
SDVLTISGTIMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHNYNILIATLRV
ALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAM
QAQQGRSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGAGAEESELQAY
IAQCQDSPTSGKFRRGSGSACSLLCCCGRDPSEEHSLLVN

Sequence length

580

Interactions

View interactions

	KEGG		Reactome
	Calcium signaling pathway Lysosome		TRP channels Transferrin endocytosis and recycling

886

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Likely pathogenic	rs2146024743	RCV001814447
Clear cell carcinoma of kidney	Pathogenic	rs104886461	RCV005887308
Lisch epithelial corneal dystrophy	Likely pathogenic; Pathogenic	rs765577483, rs1056159821, rs1368027694, rs104886461, rs121908372, rs797044824, rs767122713, rs755042147, rs797044822, rs797044823, rs2512472276, rs2022588840, rs767950930, rs1555741822	RCV005023146 RCV005014542 RCV005016942 RCV005003336 RCV005016242 RCV003985298 RCV005016546 RCV005003546 RCV005025308 RCV005016547 RCV005027972 RCV003985715 RCV005027463 RCV005027804
MCOLN1-related disorder	Likely pathogenic; Pathogenic	rs2512468099, rs121908372, rs797044818, rs148748724	RCV003903669 RCV003894792 RCV004757154 RCV004757235
Mucolipidosis	Pathogenic	rs104886461	RCV000825567
Mucolipidosis type IV	Pathogenic; Likely pathogenic	rs148748724, rs2146023425, rs2146025414, rs776845391, rs765577483, rs1056159821, rs1349755445, rs2146023956, rs2146022423, rs2146022784, rs2146024554, rs2146021332, rs2146022577, rs757685298, rs2146022877 View all (79 more)	RCV001378286 RCV001379502 RCV001378954 RCV001384670 RCV001385399 RCV001388005 RCV001380641 RCV001385590 RCV001783636 RCV001959318 RCV001875299 RCV001928601 RCV001993694 RCV002037683 RCV001994819 RCV002035280 RCV002022065 RCV002007621 RCV001962958 RCV001939516 RCV001939774 RCV001880821 RCV001995040 RCV001963290 RCV002306598 RCV002309586 RCV002307980 RCV002309031 RCV002306886 RCV002306970 RCV002307026 RCV002307065 RCV002310128 RCV002308389 RCV002624890 RCV002654679 RCV000005438 RCV000005440 RCV000005442 RCV000005443 RCV000005444 RCV000195067 RCV000192300 RCV000194725 RCV000192307 RCV000192301 RCV000192302 RCV000193040 RCV000192304 RCV002791902 RCV002825468 RCV002913936 RCV002947310 RCV003037718 RCV003029265 RCV003017136 RCV003147189 RCV001855065 RCV003484212 RCV003505845 RCV003506146 RCV003505955 RCV003506283 RCV003504730 RCV003613618 RCV003613797 RCV003614562 RCV003615464 RCV005015109 RCV004576148 RCV000410923 RCV000410945 RCV000409750 RCV000410830 RCV000411895 RCV000411871 RCV000412239 RCV000409544 RCV000412404 RCV000412421 RCV003766164 RCV001273277 RCV000673766 RCV000671408 RCV000671073 RCV000669577 RCV000664931 RCV000671858 RCV000818854 RCV001004612 RCV001004613 RCV001004614 RCV001037343 RCV001066766 RCV001223600 RCV001246653
Ovarian serous cystadenocarcinoma	Pathogenic	rs104886461	RCV005887309
Thyroid cancer, nonmedullary, 1	Pathogenic	rs104886461	RCV005887310

Show/Hide Unknown Diseases (18)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign	rs73488492	RCV005894878
Cervical cancer	Likely benign; Benign	rs75894786, rs113935640, rs28541364	RCV005915966 RCV005918473 RCV005901304
Colon adenocarcinoma	Benign; Likely benign	rs28541364	RCV005901301
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	rs2512473642	RCV004557791
Gastric cancer	Likely benign; Benign	rs111944067, rs28541364	RCV005919344 RCV005901307
Hepatocellular carcinoma	Likely benign; Benign	rs111944067, rs28541364	RCV005919342 RCV005901302
Hereditary spastic paraplegia 5A	Uncertain significance	rs1599254675	RCV000984499
Lung cancer	Likely benign; Benign	rs75894786, rs73488492, rs28541364	RCV005915967 RCV005894883 RCV005901310
Malignant lymphoma, large B-cell, diffuse	Benign	rs73488492	RCV005894880
Malignant tumor of esophagus	Likely benign; Uncertain significance; Benign	rs75894786, rs111944067, rs797044826, rs73488492, rs28541364	RCV005915965 RCV005919343 RCV005892210 RCV005894879 RCV005901303
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	rs528887619	RCV005907516
Retinal dystrophy	Conflicting classifications of pathogenicity	rs750170007	RCV004813725
Sarcoma	Benign; Likely benign	rs28541364	RCV005901306
See cases	Conflicting classifications of pathogenicity	rs886054694	RCV002252097
Squamous cell carcinoma of the head and neck	Likely benign	rs764264222	RCV005934998
Thymoma	Benign	rs73488492	RCV005894882
Uterine carcinosarcoma	Likely benign; Benign	rs111944067, rs28541364	RCV005919346 RCV005901308
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs28541364	RCV005901311

Show/Hide Text Mining Associations (31)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Agenesis of Corpus Callosum	Associate	31578829
Alzheimer Disease	Associate	36825945
Aphasia	Associate	33094427
Atrial Fibrillation	Associate	28839241
Blindness	Associate	28112729
Carcinoma Hepatocellular	Associate	35274126
Colonic Neoplasms	Associate	38188686
Corneal Dystrophy Lisch Epithelial	Associate	37972748
Eye Diseases	Associate	18326692
Genetic Diseases Inborn	Associate	22268962
Glioblastoma	Associate	35887088
Glioma	Inhibit	34878954
HIV Infections	Associate	31439883
Immunologic Deficiency Syndromes	Associate	28087698
Intellectual Disability	Associate	21224396, 28112729
Intervertebral Disc Degeneration	Associate	31827137
Lewy Body Disease	Associate	25933391
Low Back Pain	Associate	31827137
Lysosomal Storage Diseases	Associate	16361256, 16497227, 20736310, 21224396, 21613607, 23535491, 28087698, 28112729, 35131932
Melanoma	Inhibit	34878954
Mucolipidoses	Associate	11845410, 16361256, 16497227, 16645217, 17056595, 17662026, 18258208, 18326692, 18504305, 19638346, 19864416, 20159435, 20736310, 21224396, 21613607 View all (13 more)
Myopathy with Giant Abnormal Mitochondria	Stimulate	34878954
Neoplasm Metastasis	Inhibit	34878954
Neoplasms	Inhibit	34878954
Neurocognitive Disorders	Associate	31439883
Neurodegenerative Diseases	Associate	11845410, 19638346, 20736310, 27248469, 28112729, 36825945
Neurologic Manifestations	Associate	16497227, 19864416
Niemann Pick Diseases	Associate	23535491
Parkinson Disease	Associate	34250953
Retinal Dystrophies	Associate	18326692, 24332805
Tay Sachs Disease	Associate	23535491

MCOLN1 (mucolipin TRP cation channel 1)