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	6342
Gene name	Sterol carrier protein 2
Gene symbol	SCP2
Synonyms (NCBI Gene)	NLTPNSL-TPSCOXSCP-2SCP-CHISCP-XSCPX
Chromosome	1
Chromosome location	1p32.3
Summary	This gene encodes two proteins: sterol carrier protein X (SCPx) and sterol carrier protein 2 (SCP2), as a result of transcription initiation from 2 independently regulated promoters. The transcript initiated from the proximal promoter encodes the longer S

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs144132787	G>T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs148423275	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, genic upstream transcript variant, coding sequence variant
rs761545816	T>C	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, intron variant
rs774694600	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, genic upstream transcript variant
rs1572119109	->A	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant

146

Show/Hide all (146)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016091	hsa-miR-769-5p	Sequencing	20371350
MIRT030161	hsa-miR-26b-5p	Microarray	19088304
MIRT052762	hsa-miR-1260b	CLASH	23622248
MIRT563554	hsa-miR-4733-5p	PAR-CLIP	20371350
MIRT072025	hsa-miR-511-3p	PAR-CLIP	20371350
MIRT563553	hsa-miR-4762-5p	PAR-CLIP	20371350
MIRT563552	hsa-miR-622	PAR-CLIP	20371350
MIRT563551	hsa-miR-662	PAR-CLIP	20371350
MIRT072026	hsa-miR-4703-3p	PAR-CLIP	20371350
MIRT072022	hsa-miR-192-3p	PAR-CLIP	20371350
MIRT563550	hsa-miR-4776-3p	PAR-CLIP	20371350
MIRT072021	hsa-miR-30a-3p	PAR-CLIP	20371350
MIRT072023	hsa-miR-30d-3p	PAR-CLIP	20371350
MIRT072024	hsa-miR-30e-3p	PAR-CLIP	20371350
MIRT563554	hsa-miR-4733-5p	PAR-CLIP	20371350
MIRT072025	hsa-miR-511-3p	PAR-CLIP	20371350
MIRT563553	hsa-miR-4762-5p	PAR-CLIP	20371350
MIRT563552	hsa-miR-622	PAR-CLIP	20371350
MIRT563551	hsa-miR-662	PAR-CLIP	20371350
MIRT072026	hsa-miR-4703-3p	PAR-CLIP	20371350
MIRT072022	hsa-miR-192-3p	PAR-CLIP	20371350
MIRT563550	hsa-miR-4776-3p	PAR-CLIP	20371350
MIRT072021	hsa-miR-30a-3p	PAR-CLIP	20371350
MIRT072023	hsa-miR-30d-3p	PAR-CLIP	20371350
MIRT072024	hsa-miR-30e-3p	PAR-CLIP	20371350
MIRT1330574	hsa-miR-361-5p	CLIP-seq
MIRT1330575	hsa-miR-3925-5p	CLIP-seq
MIRT1330576	hsa-miR-432	CLIP-seq
MIRT1330577	hsa-miR-4453	CLIP-seq
MIRT1330578	hsa-miR-4538	CLIP-seq
MIRT1330579	hsa-miR-4712-3p	CLIP-seq
MIRT1330580	hsa-miR-873	CLIP-seq
MIRT1330581	hsa-miR-146a	CLIP-seq
MIRT1330582	hsa-miR-146b-5p	CLIP-seq
MIRT1330583	hsa-miR-203	CLIP-seq
MIRT1330584	hsa-miR-340	CLIP-seq
MIRT1330585	hsa-miR-3653	CLIP-seq
MIRT1330586	hsa-miR-3658	CLIP-seq
MIRT1330587	hsa-miR-374a	CLIP-seq
MIRT1330588	hsa-miR-374b	CLIP-seq
MIRT1330589	hsa-miR-4799-5p	CLIP-seq
MIRT1330590	hsa-miR-589	CLIP-seq
MIRT1330591	hsa-miR-660	CLIP-seq
MIRT1330581	hsa-miR-146a	CLIP-seq
MIRT1330582	hsa-miR-146b-5p	CLIP-seq
MIRT1330583	hsa-miR-203	CLIP-seq
MIRT1330592	hsa-miR-217	CLIP-seq
MIRT1330593	hsa-miR-337-3p	CLIP-seq
MIRT1330584	hsa-miR-340	CLIP-seq
MIRT1330594	hsa-miR-3616-5p	CLIP-seq
MIRT1330595	hsa-miR-3647-5p	CLIP-seq
MIRT1330587	hsa-miR-374a	CLIP-seq
MIRT1330588	hsa-miR-374b	CLIP-seq
MIRT1330596	hsa-miR-4420	CLIP-seq
MIRT1330597	hsa-miR-4461	CLIP-seq
MIRT1330598	hsa-miR-4680-3p	CLIP-seq
MIRT1330599	hsa-miR-4766-5p	CLIP-seq
MIRT1330600	hsa-miR-4795-5p	CLIP-seq
MIRT1330601	hsa-miR-519a	CLIP-seq
MIRT1330602	hsa-miR-519b-3p	CLIP-seq
MIRT1330603	hsa-miR-519c-3p	CLIP-seq
MIRT1330604	hsa-miR-539	CLIP-seq
MIRT1330605	hsa-miR-548a-3p	CLIP-seq
MIRT1330606	hsa-miR-548e	CLIP-seq
MIRT1330607	hsa-miR-548f	CLIP-seq
MIRT1330608	hsa-miR-570	CLIP-seq
MIRT1330609	hsa-miR-573	CLIP-seq
MIRT1330610	hsa-miR-580	CLIP-seq
MIRT1330590	hsa-miR-589	CLIP-seq
MIRT2097872	hsa-miR-2054	CLIP-seq
MIRT2322230	hsa-miR-297	CLIP-seq
MIRT2322231	hsa-miR-3149	CLIP-seq
MIRT2322232	hsa-miR-590-3p	CLIP-seq
MIRT2458983	hsa-miR-1261	CLIP-seq
MIRT2458984	hsa-miR-1286	CLIP-seq
MIRT2458985	hsa-miR-214	CLIP-seq
MIRT2458986	hsa-miR-2278	CLIP-seq
MIRT2458987	hsa-miR-3120-3p	CLIP-seq
MIRT2458988	hsa-miR-3145-3p	CLIP-seq
MIRT2458989	hsa-miR-3619-5p	CLIP-seq
MIRT1330575	hsa-miR-3925-5p	CLIP-seq
MIRT2458990	hsa-miR-3940-3p	CLIP-seq
MIRT1330576	hsa-miR-432	CLIP-seq
MIRT2458991	hsa-miR-4436a	CLIP-seq
MIRT1330577	hsa-miR-4453	CLIP-seq
MIRT1330578	hsa-miR-4538	CLIP-seq
MIRT1330579	hsa-miR-4712-3p	CLIP-seq
MIRT2458992	hsa-miR-4773	CLIP-seq
MIRT2458993	hsa-miR-761	CLIP-seq
MIRT2690250	hsa-miR-1228	CLIP-seq
MIRT2690251	hsa-miR-1246	CLIP-seq
MIRT2690252	hsa-miR-1273d	CLIP-seq
MIRT2690253	hsa-miR-1279	CLIP-seq
MIRT2690254	hsa-miR-1305	CLIP-seq
MIRT1330581	hsa-miR-146a	CLIP-seq
MIRT1330582	hsa-miR-146b-5p	CLIP-seq
MIRT2690255	hsa-miR-1912	CLIP-seq
MIRT2690256	hsa-miR-199a-3p	CLIP-seq
MIRT2690257	hsa-miR-199b-3p	CLIP-seq
MIRT2690258	hsa-miR-200b	CLIP-seq
MIRT2690259	hsa-miR-200c	CLIP-seq
MIRT1330583	hsa-miR-203	CLIP-seq
MIRT2097872	hsa-miR-2054	CLIP-seq
MIRT1330592	hsa-miR-217	CLIP-seq
MIRT2322230	hsa-miR-297	CLIP-seq
MIRT2690260	hsa-miR-3122	CLIP-seq
MIRT2690261	hsa-miR-3129-5p	CLIP-seq
MIRT2690262	hsa-miR-3148	CLIP-seq
MIRT2322231	hsa-miR-3149	CLIP-seq
MIRT2690263	hsa-miR-3155	CLIP-seq
MIRT2690264	hsa-miR-3155b	CLIP-seq
MIRT2690265	hsa-miR-3163	CLIP-seq
MIRT2690266	hsa-miR-3201	CLIP-seq
MIRT2690267	hsa-miR-330-3p	CLIP-seq
MIRT1330584	hsa-miR-340	CLIP-seq
MIRT1330585	hsa-miR-3653	CLIP-seq
MIRT1330586	hsa-miR-3658	CLIP-seq
MIRT2690268	hsa-miR-3662	CLIP-seq
MIRT1330587	hsa-miR-374a	CLIP-seq
MIRT1330588	hsa-miR-374b	CLIP-seq
MIRT2690269	hsa-miR-374c	CLIP-seq
MIRT2690270	hsa-miR-3913-5p	CLIP-seq
MIRT2690271	hsa-miR-4275	CLIP-seq
MIRT2690272	hsa-miR-429	CLIP-seq
MIRT2690273	hsa-miR-4496	CLIP-seq
MIRT2690274	hsa-miR-452	CLIP-seq
MIRT2690275	hsa-miR-4676-3p	CLIP-seq
MIRT2690276	hsa-miR-4716-5p	CLIP-seq
MIRT2690277	hsa-miR-4738-3p	CLIP-seq
MIRT2690278	hsa-miR-4747-5p	CLIP-seq
MIRT2690279	hsa-miR-4762-3p	CLIP-seq
MIRT1330599	hsa-miR-4766-5p	CLIP-seq
MIRT2690280	hsa-miR-4791	CLIP-seq
MIRT2690281	hsa-miR-484	CLIP-seq
MIRT2690282	hsa-miR-498	CLIP-seq
MIRT2690283	hsa-miR-509-3p	CLIP-seq
MIRT1330605	hsa-miR-548a-3p	CLIP-seq
MIRT2690284	hsa-miR-548c-3p	CLIP-seq
MIRT1330606	hsa-miR-548e	CLIP-seq
MIRT1330607	hsa-miR-548f	CLIP-seq
MIRT1330608	hsa-miR-570	CLIP-seq
MIRT1330590	hsa-miR-589	CLIP-seq
MIRT2322232	hsa-miR-590-3p	CLIP-seq
MIRT2690285	hsa-miR-655	CLIP-seq
MIRT1330591	hsa-miR-660	CLIP-seq
MIRT2690286	hsa-miR-944	CLIP-seq

Show/Hide all (65)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000062	Function	Fatty-acyl-CoA binding	IDA	18465878
GO:0003988	Function	Acetyl-CoA C-acyltransferase activity	IEA
GO:0003988	Function	Acetyl-CoA C-acyltransferase activity	ISS
GO:0005102	Function	Signaling receptor binding	IPI	21375735
GO:0005515	Function	Protein binding	IPI	15182174, 19584060, 21516116, 25416956, 32814053
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	ISS
GO:0005777	Component	Peroxisome	IBA
GO:0005777	Component	Peroxisome	IDA	1347505, 21375735
GO:0005777	Component	Peroxisome	IEA
GO:0005777	Component	Peroxisome	ISS
GO:0005782	Component	Peroxisomal matrix	ISS
GO:0005782	Component	Peroxisomal matrix	TAS
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	ISS
GO:0005829	Component	Cytosol	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006635	Process	Fatty acid beta-oxidation	ISS
GO:0006636	Process	Unsaturated fatty acid biosynthetic process	IEA
GO:0006694	Process	Steroid biosynthetic process	IDA	1703300
GO:0006699	Process	Bile acid biosynthetic process	TAS
GO:0006701	Process	Progesterone biosynthetic process	IDA	1703300
GO:0006869	Process	Lipid transport	IEA
GO:0008206	Process	Bile acid metabolic process	ISS
GO:0008289	Function	Lipid binding	IEA
GO:0008526	Function	Phosphatidylinositol transfer activity	IDA	12641450
GO:0015485	Function	Cholesterol binding	IDA	18465878
GO:0015914	Process	Phospholipid transport	IDA	12641450
GO:0015914	Process	Phospholipid transport	IEA
GO:0015918	Process	Sterol transport	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0016747	Function	Acyltransferase activity, transferring groups other than amino-acyl groups	IEA
GO:0019216	Process	Regulation of lipid metabolic process	IEA
GO:0032367	Process	Intracellular cholesterol transport	IMP	7642518
GO:0032385	Process	Positive regulation of intracellular cholesterol transport	IDA	15449949
GO:0032385	Process	Positive regulation of intracellular cholesterol transport	NAS	1703300
GO:0032959	Process	Inositol trisphosphate biosynthetic process	IDA	12641450
GO:0032991	Component	Protein-containing complex	IDA	19584060
GO:0033540	Process	Fatty acid beta-oxidation using acyl-CoA oxidase	TAS
GO:0033814	Function	Propanoyl-CoA C-acyltransferase activity	IEA
GO:0036042	Function	Long-chain fatty acyl-CoA binding	IDA	17418802
GO:0036109	Process	Alpha-linolenic acid metabolic process	IEA
GO:0036109	Process	Alpha-linolenic acid metabolic process	TAS
GO:0042759	Process	Long-chain fatty acid biosynthetic process	IEA
GO:0045940	Process	Positive regulation of steroid metabolic process	IDA	1703300
GO:0050632	Function	Propionyl-CoA C2-trimethyltridecanoyltransferase activity	EXP	9245689, 11734571, 16685654
GO:0050632	Function	Propionyl-CoA C2-trimethyltridecanoyltransferase activity	IEA
GO:0050632	Function	Propionyl-CoA C2-trimethyltridecanoyltransferase activity	ISS
GO:0050632	Function	Propionyl-CoA C2-trimethyltridecanoyltransferase activity	TAS
GO:0050633	Function	Acetyl-CoA C-myristoyltransferase activity	IEA
GO:0050633	Function	Acetyl-CoA C-myristoyltransferase activity	ISS
GO:0070538	Function	Oleic acid binding	IDA	18465878
GO:0071071	Process	Regulation of phospholipid biosynthetic process	ISS
GO:0072659	Process	Protein localization to plasma membrane	IDA	12641450
GO:0120009	Process	Intermembrane lipid transfer	IEA
GO:0120019	Function	Phosphatidylcholine transfer activity	ISS
GO:0120020	Function	Cholesterol transfer activity	IMP	7642518
GO:0120020	Function	Cholesterol transfer activity	ISS
GO:1901373	Process	Lipid hydroperoxide transport	IDA	15449949
GO:1901570	Process	Fatty acid derivative biosynthetic process	IEA

MIM	HGNC	e!Ensembl
184755	10606	ENSG00000116171

P22307

Protein name

Sterol carrier protein 2 (SCP-2) (Acetyl-CoA C-myristoyltransferase) (EC 2.3.1.155) (Non-specific lipid-transfer protein) (NSL-TP) (Propanoyl-CoA C-acyltransferase) (EC 2.3.1.176) (SCP-2/3-oxoacyl-CoA thiolase) (SCP-2/thiolase) (EC 2.3.1.16) (SCP-chi) (SC

Protein function

[Isoform SCPx]: Plays a crucial role in the peroxisomal oxidation of branched-chain fatty acids (PubMed:10706581). Catalyzes the last step of the peroxisomal beta-oxidation of branched chain fatty acids and the side chain of the bile acid interm

PDB

1QND , 2C0L

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00108	Thiolase_N	14 → 240	Thiolase, N-terminal domain	Domain
PF02803	Thiolase_C	279 → 401	Thiolase, C-terminal domain	Domain
PF02036	SCP2	437 → 539	SCP-2 sterol transfer family	Family

Tissue specificity

TISSUE SPECIFICITY: Liver, fibroblasts, and placenta.

Sequence

MSSSPWEPATLRRVFVVGVGMTKFVKPGAENSRDYPDLAEEAGKKALADAQIPYSAVDQA
CVGYVFGDSTCGQRAIYHSLGMTGIPIINVNNNCATGSTALFMARQLIQGGVAECVLALG
FEKMSKGSLGIKFSDRTIPTDKHVDLLINKYGLSAHPVAPQMFGYAGKEHMEKYGTKIEH
FAKIGWKNHKHSVNNPYSQFQDEYSLDEVMASKEVFDFLTILQCCPTSDGAAAAILASEA
FVQKYGLQSKAVEILAQEMMTDLPSSFEEKSIIKMVGFDMSKEAARKCYEKSGLTPNDID
VIELHDCFSTNELLTYEALGLCPEGQGATLVDRGDNTYGGKWVINPSGGLISKGHPLGAT
GLAQCAELCWQLRGEAGKRQVPGAKVALQHNLGIGGAVVVTLYKMGFPEAASSFRTHQIE
AVPTSSASDGFKANLVFKEIEKKLEEEGEQFVKKIGGIFAFKVKDGPGGKEATWVVDVKN
GKGSVLPNSDKKADCTITMADSDFLALMTGKMNPQSAFFQGKLKITGNMGLAMKLQNLQL
QPGNAKL

Sequence length

547

Interactions

View interactions

	KEGG		Reactome
	Primary bile acid biosynthesis Biosynthesis of unsaturated fatty acids Metabolic pathways Fatty acid metabolism PPAR signaling pathway Peroxisome		Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol alpha-linolenic acid (ALA) metabolism Beta-oxidation of pristanoyl-CoA Peroxisomal protein import

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hepatocellular carcinoma	Likely pathogenic; Pathogenic	rs144132787	RCV005898546	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ovarian cancer	Likely pathogenic; Pathogenic	rs144132787	RCV005898547	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SCP2-related disorder	Pathogenic; Likely pathogenic	rs369561869, rs144132787	RCV004731130 RCV003409851	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sterol carrier protein 2 deficiency	Pathogenic; Likely pathogenic	rs369561869, rs772506944, rs1572119109, rs144132787	RCV001336527 RCV003387544 RCV000013658 RCV000578448	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
DEFICIENCY OF STEROL CARRIER PROTEIN X	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leukodystrophy	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Melanoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYNEUROPATHIES	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYNEUROPATHY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENSORINEURAL HEARING LOSS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sensorineural hearing loss disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

SCP2 (sterol carrier protein 2)