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	10577
Gene name	NPC intracellular cholesterol transporter 2
Gene symbol	NPC2
Synonyms (NCBI Gene)	EDDM1HE1
Chromosome	14
Chromosome location	14q24.3
Summary	This gene encodes a protein containing a lipid recognition domain. The encoded protein may function in regulating the transport of cholesterol through the late endosomal/lysosomal system. Mutations in this gene have been associated with Niemann-Pick disea

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs11694	A>G	Pathogenic	Coding sequence variant, missense variant
rs80358261	C>T	Pathogenic	Missense variant, coding sequence variant
rs80358262	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs80358263	G>T	Pathogenic	Stop gained, coding sequence variant
rs80358264	A>G	Pathogenic	Missense variant, coding sequence variant
rs80358266	C>A,T	Pathogenic, uncertain-significance	Stop gained, coding sequence variant, missense variant
rs80358268	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs104894458	G>A	Pathogenic	Missense variant, coding sequence variant
rs151220873	C>T	Benign, benign-likely-benign, likely-pathogenic	Coding sequence variant, missense variant
rs1555345873	TCTA>-	Likely-pathogenic	Splice acceptor variant, coding sequence variant, intron variant

157

Show/Hide all (157)

miRTarBase ID	miRNA	Experiments	Reference
MIRT049322	hsa-miR-92a-3p	CLASH	23622248
MIRT1190538	hsa-miR-2053	CLIP-seq
MIRT1190539	hsa-miR-302a	CLIP-seq
MIRT1190540	hsa-miR-302b	CLIP-seq
MIRT1190541	hsa-miR-302c	CLIP-seq
MIRT1190542	hsa-miR-302d	CLIP-seq
MIRT1190543	hsa-miR-302e	CLIP-seq
MIRT1190544	hsa-miR-3180-5p	CLIP-seq
MIRT1190545	hsa-miR-335	CLIP-seq
MIRT1190546	hsa-miR-372	CLIP-seq
MIRT1190547	hsa-miR-373	CLIP-seq
MIRT1190548	hsa-miR-3934	CLIP-seq
MIRT1190549	hsa-miR-409-3p	CLIP-seq
MIRT1190550	hsa-miR-4272	CLIP-seq
MIRT1190551	hsa-miR-4686	CLIP-seq
MIRT1190552	hsa-miR-4717-5p	CLIP-seq
MIRT1190553	hsa-miR-512-3p	CLIP-seq
MIRT1190554	hsa-miR-513a-3p	CLIP-seq
MIRT1190555	hsa-miR-520a-3p	CLIP-seq
MIRT1190556	hsa-miR-520b	CLIP-seq
MIRT1190557	hsa-miR-520c-3p	CLIP-seq
MIRT1190558	hsa-miR-520d-3p	CLIP-seq
MIRT1190559	hsa-miR-520e	CLIP-seq
MIRT1190560	hsa-miR-569	CLIP-seq
MIRT1190561	hsa-miR-583	CLIP-seq
MIRT2055168	hsa-miR-127-5p	CLIP-seq
MIRT2055169	hsa-miR-214	CLIP-seq
MIRT2055170	hsa-miR-3187-3p	CLIP-seq
MIRT1190545	hsa-miR-335	CLIP-seq
MIRT2055171	hsa-miR-3619-5p	CLIP-seq
MIRT2055172	hsa-miR-4291	CLIP-seq
MIRT2055173	hsa-miR-4435	CLIP-seq
MIRT2055174	hsa-miR-4701-5p	CLIP-seq
MIRT2055175	hsa-miR-4771	CLIP-seq
MIRT2055176	hsa-miR-548s	CLIP-seq
MIRT2055177	hsa-miR-588	CLIP-seq
MIRT2055178	hsa-miR-761	CLIP-seq
MIRT2055179	hsa-miR-922	CLIP-seq
MIRT2284116	hsa-miR-1203	CLIP-seq
MIRT2284117	hsa-miR-1208	CLIP-seq
MIRT2055169	hsa-miR-214	CLIP-seq
MIRT1190544	hsa-miR-3180-5p	CLIP-seq
MIRT2055170	hsa-miR-3187-3p	CLIP-seq
MIRT1190545	hsa-miR-335	CLIP-seq
MIRT2284118	hsa-miR-3617	CLIP-seq
MIRT2055171	hsa-miR-3619-5p	CLIP-seq
MIRT2284119	hsa-miR-3670	CLIP-seq
MIRT1190548	hsa-miR-3934	CLIP-seq
MIRT2055172	hsa-miR-4291	CLIP-seq
MIRT2284120	hsa-miR-4311	CLIP-seq
MIRT2284121	hsa-miR-4328	CLIP-seq
MIRT2055173	hsa-miR-4435	CLIP-seq
MIRT2284122	hsa-miR-4691-3p	CLIP-seq
MIRT2055174	hsa-miR-4701-5p	CLIP-seq
MIRT2055175	hsa-miR-4771	CLIP-seq
MIRT2284123	hsa-miR-501-3p	CLIP-seq
MIRT2284124	hsa-miR-502-3p	CLIP-seq
MIRT1190554	hsa-miR-513a-3p	CLIP-seq
MIRT2055176	hsa-miR-548s	CLIP-seq
MIRT1190561	hsa-miR-583	CLIP-seq
MIRT2055177	hsa-miR-588	CLIP-seq
MIRT2284125	hsa-miR-589	CLIP-seq
MIRT2284126	hsa-miR-641	CLIP-seq
MIRT2055178	hsa-miR-761	CLIP-seq
MIRT2055179	hsa-miR-922	CLIP-seq
MIRT2284116	hsa-miR-1203	CLIP-seq
MIRT2582200	hsa-miR-146a	CLIP-seq
MIRT2582201	hsa-miR-146b-5p	CLIP-seq
MIRT2582202	hsa-miR-1827	CLIP-seq
MIRT2055169	hsa-miR-214	CLIP-seq
MIRT2582203	hsa-miR-221	CLIP-seq
MIRT2582204	hsa-miR-222	CLIP-seq
MIRT1190544	hsa-miR-3180-5p	CLIP-seq
MIRT2055170	hsa-miR-3187-3p	CLIP-seq
MIRT1190545	hsa-miR-335	CLIP-seq
MIRT2284118	hsa-miR-3617	CLIP-seq
MIRT2055171	hsa-miR-3619-5p	CLIP-seq
MIRT2582205	hsa-miR-3663-3p	CLIP-seq
MIRT2284119	hsa-miR-3670	CLIP-seq
MIRT1190548	hsa-miR-3934	CLIP-seq
MIRT1190549	hsa-miR-409-3p	CLIP-seq
MIRT2582206	hsa-miR-4251	CLIP-seq
MIRT1190550	hsa-miR-4272	CLIP-seq
MIRT2055172	hsa-miR-4291	CLIP-seq
MIRT2284120	hsa-miR-4311	CLIP-seq
MIRT2284121	hsa-miR-4328	CLIP-seq
MIRT2055173	hsa-miR-4435	CLIP-seq
MIRT2284122	hsa-miR-4691-3p	CLIP-seq
MIRT2055174	hsa-miR-4701-5p	CLIP-seq
MIRT1190552	hsa-miR-4717-5p	CLIP-seq
MIRT2055175	hsa-miR-4771	CLIP-seq
MIRT2582207	hsa-miR-4797-5p	CLIP-seq
MIRT2284123	hsa-miR-501-3p	CLIP-seq
MIRT2284124	hsa-miR-502-3p	CLIP-seq
MIRT1190554	hsa-miR-513a-3p	CLIP-seq
MIRT2582208	hsa-miR-544	CLIP-seq
MIRT2055176	hsa-miR-548s	CLIP-seq
MIRT2582209	hsa-miR-548v	CLIP-seq
MIRT1190560	hsa-miR-569	CLIP-seq
MIRT1190561	hsa-miR-583	CLIP-seq
MIRT2055177	hsa-miR-588	CLIP-seq
MIRT2284125	hsa-miR-589	CLIP-seq
MIRT2284126	hsa-miR-641	CLIP-seq
MIRT2055178	hsa-miR-761	CLIP-seq
MIRT2055179	hsa-miR-922	CLIP-seq
MIRT2582210	hsa-miR-95	CLIP-seq
MIRT2284116	hsa-miR-1203	CLIP-seq
MIRT2686452	hsa-miR-1243	CLIP-seq
MIRT2686453	hsa-miR-1270	CLIP-seq
MIRT2582200	hsa-miR-146a	CLIP-seq
MIRT2582201	hsa-miR-146b-5p	CLIP-seq
MIRT2582202	hsa-miR-1827	CLIP-seq
MIRT2686454	hsa-miR-185	CLIP-seq
MIRT1190538	hsa-miR-2053	CLIP-seq
MIRT2055169	hsa-miR-214	CLIP-seq
MIRT2582203	hsa-miR-221	CLIP-seq
MIRT2582204	hsa-miR-222	CLIP-seq
MIRT2686455	hsa-miR-224	CLIP-seq
MIRT1190544	hsa-miR-3180-5p	CLIP-seq
MIRT2055170	hsa-miR-3187-3p	CLIP-seq
MIRT1190545	hsa-miR-335	CLIP-seq
MIRT2686456	hsa-miR-34b	CLIP-seq
MIRT2284118	hsa-miR-3617	CLIP-seq
MIRT2055171	hsa-miR-3619-5p	CLIP-seq
MIRT2582205	hsa-miR-3663-3p	CLIP-seq
MIRT2284119	hsa-miR-3670	CLIP-seq
MIRT1190548	hsa-miR-3934	CLIP-seq
MIRT1190549	hsa-miR-409-3p	CLIP-seq
MIRT2582206	hsa-miR-4251	CLIP-seq
MIRT1190550	hsa-miR-4272	CLIP-seq
MIRT2055172	hsa-miR-4291	CLIP-seq
MIRT2686457	hsa-miR-4306	CLIP-seq
MIRT2284120	hsa-miR-4311	CLIP-seq
MIRT2284121	hsa-miR-4328	CLIP-seq
MIRT2055173	hsa-miR-4435	CLIP-seq
MIRT2686458	hsa-miR-4531	CLIP-seq
MIRT2686459	hsa-miR-4644	CLIP-seq
MIRT2284122	hsa-miR-4691-3p	CLIP-seq
MIRT2055174	hsa-miR-4701-5p	CLIP-seq
MIRT1190552	hsa-miR-4717-5p	CLIP-seq
MIRT2055175	hsa-miR-4771	CLIP-seq
MIRT2582207	hsa-miR-4797-5p	CLIP-seq
MIRT2284123	hsa-miR-501-3p	CLIP-seq
MIRT2284124	hsa-miR-502-3p	CLIP-seq
MIRT1190554	hsa-miR-513a-3p	CLIP-seq
MIRT2582208	hsa-miR-544	CLIP-seq
MIRT2055176	hsa-miR-548s	CLIP-seq
MIRT2582209	hsa-miR-548v	CLIP-seq
MIRT1190560	hsa-miR-569	CLIP-seq
MIRT1190561	hsa-miR-583	CLIP-seq
MIRT2055177	hsa-miR-588	CLIP-seq
MIRT2284125	hsa-miR-589	CLIP-seq
MIRT2686460	hsa-miR-620	CLIP-seq
MIRT2284126	hsa-miR-641	CLIP-seq
MIRT2055178	hsa-miR-761	CLIP-seq
MIRT2055179	hsa-miR-922	CLIP-seq
MIRT2582210	hsa-miR-95	CLIP-seq

Show/Hide all (43)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	19664597, 20674861, 22095670, 27238017, 27940359
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IMP	15937921
GO:0005764	Component	Lysosome	IDA	25339683
GO:0005764	Component	Lysosome	IDA	11125141, 15937921
GO:0005764	Component	Lysosome	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006869	Process	Lipid transport	IEA
GO:0008202	Process	Steroid metabolic process	IEA
GO:0008203	Process	Cholesterol metabolic process	IEA
GO:0009615	Process	Response to virus	IEP	16548883
GO:0010467	Process	Gene expression	IEA
GO:0010878	Process	Cholesterol storage	IEA
GO:0015485	Function	Cholesterol binding	IBA
GO:0015485	Function	Cholesterol binding	IDA	17018531, 18772377, 27238017
GO:0015485	Function	Cholesterol binding	IEA
GO:0015914	Process	Phospholipid transport	TAS	17018531
GO:0015918	Process	Sterol transport	IEA
GO:0015918	Process	Sterol transport	IEA
GO:0016125	Process	Sterol metabolic process	IEA
GO:0019747	Process	Regulation of isoprenoid metabolic process	TAS	15110773
GO:0019899	Function	Enzyme binding	IPI	15110773
GO:0030301	Process	Cholesterol transport	IDA	17018531, 18772377
GO:0030301	Process	Cholesterol transport	IEA
GO:0032366	Process	Intracellular sterol transport	IDA	17018531
GO:0032367	Process	Intracellular cholesterol transport	IBA
GO:0032367	Process	Intracellular cholesterol transport	IDA	17018531, 18823126
GO:0032367	Process	Intracellular cholesterol transport	IEA
GO:0032367	Process	Intracellular cholesterol transport	IGI	19723497
GO:0032367	Process	Intracellular cholesterol transport	IMP	15937921, 27238017
GO:0032934	Function	Sterol binding	IEA
GO:0033344	Process	Cholesterol efflux	IBA
GO:0033344	Process	Cholesterol efflux	IDA	16141411, 25339683
GO:0033344	Process	Cholesterol efflux	IEA
GO:0035578	Component	Azurophil granule lumen	TAS
GO:0042632	Process	Cholesterol homeostasis	IDA	12719428
GO:0042632	Process	Cholesterol homeostasis	IMP	15937921
GO:0043202	Component	Lysosomal lumen	TAS
GO:0046836	Process	Glycolipid transport	TAS	17018531
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0120020	Function	Cholesterol transfer activity	IDA	18772377, 25339683, 27238017

MIM	HGNC	e!Ensembl
601015	14537	ENSG00000119655

P61916

Protein name

NPC intracellular cholesterol transporter 2 (Epididymal secretory protein E1) (Human epididymis-specific protein 1) (He1) (Niemann-Pick disease type C2 protein)

Protein function

Intracellular cholesterol transporter which acts in concert with NPC1 and plays an important role in the egress of cholesterol from the lysosomal compartment (PubMed:11125141, PubMed:15937921, PubMed:17018531, PubMed:18772377, PubMed:29580834).

PDB

5KWY , 6W5V

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02221	E1_DerP2_DerF2	21 → 147	ML domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Detected in gallbladder bile (PubMed:21315718). Detected in fibroblasts, kidney, liver, spleen, small intestine, placenta and testis (at protein level) (PubMed:11125141). Epididymis. {ECO:0000269|PubMed:11125141, ECO:0000269|PubMed:196

Sequence

MRFLAATFLLLALSTAAQAEPVQFKDCGSVDGVIKEVNVSPCPTQPCQLSKGQSYSVNVT
FTSNIQSKSSKAVVHGILMGVPVPFPIPEPDGCKSGINCPIQKDKTYSYLNKLPVKSEYP
SIKLVVEWQLQDDKNQSLFCWEIPVQIVSHL

Sequence length

151

Interactions

View interactions

	KEGG		Reactome
	Lysosome Cholesterol metabolism		Neutrophil degranulation LDL clearance

284

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Niemann-Pick disease, type C	Likely pathogenic; Pathogenic	rs1376058648, rs483352893, rs80358260, rs80358266, rs104894457, rs104894458, rs80358262, rs80358264	RCV003120598 RCV003330496 RCV000586093 RCV001193596 RCV002468967 RCV005406732 RCV001193595 RCV003398552
Niemann-Pick disease, type C1	Likely pathogenic; Pathogenic	rs104894458	RCV001528117
Niemann-Pick disease, type C2	Likely pathogenic; Pathogenic	rs1376058648, rs2086687936, rs483352893, rs2139668010, rs2139670174, rs2086712268, rs2506104570, rs2506104379, rs2506115412, rs2506107075, rs2506107168, rs2506104627, rs2506107182, rs2506107370, rs1555346368 View all (32 more)	RCV001388699 RCV001806310 RCV000119339 RCV001953743 RCV001970052 RCV001963172 RCV002309655 RCV002309790 RCV002308281 RCV002309152 RCV002309360 RCV002306854 RCV002310526 RCV002308421 RCV002613296 RCV003009852 RCV000008998 RCV000009000 RCV000009001 RCV000009003 RCV000009006 RCV000009007 RCV000234869 RCV003333265 RCV003337786 RCV003486330 RCV003510699 RCV003511027 RCV003510281 RCV003620768 RCV003621234 RCV003842730 RCV004577417 RCV000020643 RCV000020644 RCV000020645 RCV000020646 RCV000020647 RCV000668992 RCV000668937 RCV000665605 RCV000670585 RCV000673729 RCV000670039 RCV000796954 RCV001061725 RCV001170047 RCV001263847 RCV001263848 RCV001263849 RCV001263850 RCV001263851
Nonpapillary renal cell carcinoma	Likely pathogenic	rs2086686955	RCV005931257

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Malignant tumor of esophagus	Benign; Likely benign	rs189666920	RCV005892850
NPC2-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	rs1025180543, rs970173671, rs80358261, rs374489111, rs139314541, rs2506115760, rs2506099906, rs142075589, rs142858704, rs1011669605, rs752818745, rs756433737	RCV003963274 RCV004756259 RCV003407307 RCV003909934 RCV003408644 RCV003894139 RCV003969656 RCV004755868 RCV003912600 RCV003945383 RCV003905881 RCV003945958
Ovarian serous cystadenocarcinoma	Uncertain significance	rs927248655	RCV005925454

Show/Hide Text Mining Associations (43)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Abdominal Injuries	Associate	32286426
Alzheimer Disease	Associate	17387528
Arthritis Rheumatoid	Associate	21084287
Atrial Fibrillation	Associate	36226239
Breast Neoplasms	Associate	20030805
Breast Neoplasms	Stimulate	24147030
Carcinoma Hepatocellular	Inhibit	24147030
Carcinoma Intraductal Noninfiltrating	Associate	20030805
Carcinoma Renal Cell	Inhibit	24147030
Citrullinemia	Associate	40003936
Colorectal Neoplasms	Associate	23203071
Colorectal Neoplasms	Stimulate	29096354
Coronary Artery Disease	Associate	39614436
Death	Associate	11567215
Dementia	Associate	27549128
Elliptocytosis Hereditary	Associate	32807033
Fibrosis	Stimulate	24147030
Fused Kidney	Associate	33590792
Gastrointestinal Neoplasms	Associate	39690926
Glaucoma Open Angle	Associate	29847670
Heredodegenerative Disorders Nervous System	Associate	11567215
Hydrops Fetalis	Associate	27549128
Inflammation	Associate	21084287, 23814065, 27402802
Intestinal Pseudo Obstruction	Associate	26666848
Latent Infection	Associate	34685683
Liver Cirrhosis	Inhibit	24147030, 29874879
Lung Diseases	Associate	11567215, 33938663
Lung Neoplasms	Associate	34685683
Lysosomal Storage Diseases	Associate	39596250, 40003936
Mitochondrial Diseases	Associate	27402802, 35159316
Neoplasms	Associate	24147030, 29096354, 35669791, 39690926
Neurodegenerative Diseases	Associate	32880929
Neurologic Manifestations	Associate	11567215
Niemann Pick Disease Type C	Associate	10521297, 11567215, 12719428, 21084287, 23144769, 23773996, 24386122, 24907126, 24915861, 25479233, 26666848, 27238017, 27366019, 27900365, 28222799 View all (16 more)
Niemann Pick disease type C2	Associate	33924575
Pulmonary Alveolar Proteinosis	Associate	39789920
Pulmonary Disease Chronic Obstructive	Associate	39690926
Respiratory Insufficiency	Associate	11567215
Stomach Neoplasms	Associate	38001127, 38025711
Sveinsson Chorioretinal Atrophy	Associate	32286426
Thyroid Neoplasms	Associate	36933059
Tuberculosis	Inhibit	24501203
Tuberculosis Meningeal	Associate	34685683

NPC2 (NPC intracellular cholesterol transporter 2)