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SCP2 sterol carrier protein 2 [ Homo sapiens (human) ]

Gene ID: 6342, updated on 5-May-2020

Summary

Official Symbol
SCP2provided by HGNC
Official Full Name
sterol carrier protein 2provided by HGNC
Primary source
HGNC:HGNC:10606
See related
Ensembl:ENSG00000116171 MIM:184755
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
NLTP; SCPX; SCP-2; SCP-X; NSL-TP; SCP-CHI
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 SCPx protein, and the transcript initiated from the distal promoter encodes the shorter SCP2 protein, with the 2 proteins sharing a common C-terminus. Evidence suggests that the SCPx protein is a peroxisome-associated thiolase that is involved in the oxidation of branched chain fatty acids, while the SCP2 protein is thought to be an intracellular lipid transfer protein. This gene is highly expressed in organs involved in lipid metabolism, and may play a role in Zellweger syndrome, in which cells are deficient in peroxisomes and have impaired bile acid synthesis. Alternative splicing of this gene produces multiple transcript variants, some encoding different isoforms.[provided by RefSeq, Aug 2010]
Expression
Ubiquitous expression in liver (RPKM 77.0), duodenum (RPKM 30.8) and 24 other tissues See more
Orthologs

Genomic context

See SCP2 in Genome Data Viewer
Location:
1p32.3
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (52927229..53051698)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53392901..53517289)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene enoyl-CoA hydratase domain containing 2 Neighboring gene translation machinery-associated protein 7 pseudogene Neighboring gene ATP synthase membrane subunit 6.8PL 0pseudogene Neighboring gene H3 histone pseudogene 2 Neighboring gene RRAS2 pseudogene 1 Neighboring gene tubulin beta class I pseudogene 10 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 11 Neighboring gene podocan Neighboring gene solute carrier family 1 member 7 Neighboring gene VISTA enhancer hs2585

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686C12188, DKFZp686D11188

Gene Ontology Provided by GOA

Function Evidence Code Pubs
acetyl-CoA C-acyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
acetyl-CoA C-myristoyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
cholesterol binding IDA
Inferred from Direct Assay
more info
PubMed 
fatty-acyl-CoA binding IDA
Inferred from Direct Assay
more info
PubMed 
long-chain fatty acyl-CoA binding IDA
Inferred from Direct Assay
more info
PubMed 
oleic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
propanoyl-CoA C-acyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
propionyl-CoA C2-trimethyltridecanoyltransferase activity EXP
Inferred from Experiment
more info
PubMed 
propionyl-CoA C2-trimethyltridecanoyltransferase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
sterol binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
alpha-linolenic acid metabolic process TAS
Traceable Author Statement
more info
 
bile acid biosynthetic process TAS
Traceable Author Statement
more info
 
bile acid metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
fatty acid beta-oxidation ISS
Inferred from Sequence or Structural Similarity
more info
 
fatty acid beta-oxidation using acyl-CoA oxidase TAS
Traceable Author Statement
more info
 
lipid hydroperoxide transport IDA
Inferred from Direct Assay
more info
PubMed 
phospholipid transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of intracellular cholesterol transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of intracellular cholesterol transport IDA
Inferred from Direct Assay
more info
PubMed 
protein targeting to peroxisome TAS
Traceable Author Statement
more info
 
steroid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
peroxisomal matrix TAS
Traceable Author Statement
more info
 
peroxisome IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
non-specific lipid-transfer protein
Names
epididymis secretory sperm binding protein
propanoyl-CoA C-acyltransferase
sterol carrier protein X
NP_001007099.1
NP_001007100.1
NP_001007101.1
NP_001007251.1
NP_001180528.1
NP_001180529.1
NP_001180546.1
NP_001317516.1
NP_002970.2
XP_005271160.1
XP_011540237.1

NCBI Reference Sequences (RefSeq)

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

  1. NG_012211.1 RefSeqGene

    Range
    5001..129423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001007098.2NP_001007099.1  non-specific lipid-transfer protein isoform 2

    See identical proteins and their annotated locations for NP_001007099.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1. It is unknown whether this isoform (2) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AC099677, AL445183, BC067108, DC330171
    Consensus CDS
    CCDS41338.1
    UniProtKB/Swiss-Prot
    P22307
    Related
    ENSP00000360568.5, ENST00000371513.9
    Conserved Domains (1) summary
    cl27752
    Location:12317
    PRK06064; acetyl-CoA acetyltransferase; Provisional
  2. NM_001007099.3NP_001007100.1  non-specific lipid-transfer protein isoform 5 precursor

    See identical proteins and their annotated locations for NP_001007100.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) results from transcription initiation from a downstream promoter. This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (5, also known as SCP2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AA664009, AB208789, AL445183, BC005911, M55421
    Consensus CDS
    CCDS44149.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000396413.2, ENST00000435345.6
    Conserved Domains (1) summary
    pfam02036
    Location:48134
    SCP2; SCP-2 sterol transfer family
  3. NM_001007100.3NP_001007101.1  non-specific lipid-transfer protein isoform 4

    See identical proteins and their annotated locations for NP_001007101.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) results from transcription initiation from a downstream promoter. This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1. It is unknown whether this isoform (4) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, AL445183, DB459183, M55421
    Consensus CDS
    CCDS44150.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000406636.2, ENST00000430330.6
    Conserved Domains (1) summary
    pfam02036
    Location:45131
    SCP2; SCP-2 sterol transfer family
  4. NM_001007250.2NP_001007251.1  non-specific lipid-transfer protein isoform 3

    See identical proteins and their annotated locations for NP_001007251.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) results from transcription initiation from a downstream promoter. This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1. It is unknown whether this isoform (3) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, CA867670, M55421
    Consensus CDS
    CCDS30719.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000386214.3, ENST00000408941.7
  5. NM_001193599.2NP_001180528.1  non-specific lipid-transfer protein isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (7) is shorter than isoform 1. It is unknown whether this isoform (7) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, AK294631, AL445183, DC330171
    Consensus CDS
    CCDS53318.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000384569.2, ENST00000407246.6
    Conserved Domains (3) summary
    PRK08256
    Location:12380
    PRK08256; lipid-transfer protein; Provisional
    cd00826
    Location:17379
    nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
    pfam02036
    Location:428514
    SCP2; SCP-2 sterol transfer family
  6. NM_001193600.2NP_001180529.1  non-specific lipid-transfer protein isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (6) is shorter than isoform 1. It is unknown whether this isoform (6) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, AC099677, AK308105, AL445183, DC330171
    Consensus CDS
    CCDS53317.1
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000360564.4, ENST00000371509.8
    Conserved Domains (3) summary
    PRK08256
    Location:12360
    PRK08256; lipid-transfer protein; Provisional
    pfam02036
    Location:408494
    SCP2; SCP-2 sterol transfer family
    cl09938
    Location:17359
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
  7. NM_001193617.2NP_001180546.1  non-specific lipid-transfer protein isoform 8

    See identical proteins and their annotated locations for NP_001180546.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (8) has a shorter N-terminus, compared to isoform 1. It is unknown whether this isoform (8) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, AK295214, AL445183, DC330171
    Consensus CDS
    CCDS53319.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000434132.1, ENST00000528311.5
    Conserved Domains (2) summary
    pfam02036
    Location:371457
    SCP2; SCP-2 sterol transfer family
    cl09938
    Location:1322
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
  8. NM_001330587.1NP_001317516.1  non-specific lipid-transfer protein isoform 9

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (9) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC099677, AL445183
    Consensus CDS
    CCDS81325.1
    UniProtKB/TrEMBL
    E9PLD1
    Related
    ENSP00000435194.1, ENST00000478631.6
  9. NM_002979.5NP_002970.2  non-specific lipid-transfer protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_002970.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as SCPx).
    Source sequence(s)
    AA664009, AB208789, AK312856, AL445183, DC330171
    Consensus CDS
    CCDS572.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    B2R761, Q59HG9
    Related
    ENSP00000360569.3, ENST00000371514.8
    Conserved Domains (2) summary
    PRK08256
    Location:12404
    PRK08256; lipid-transfer protein; Provisional
    pfam02036
    Location:452538
    SCP2; SCP-2 sterol transfer family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    52927229..53051698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005271103.4XP_005271160.1  non-specific lipid-transfer protein isoform X1

    See identical proteins and their annotated locations for XP_005271160.1

    Conserved Domains (2) summary
    PRK08256
    Location:12404
    PRK08256; lipid-transfer protein; Provisional
    cd00826
    Location:17403
    nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
  2. XM_011541935.2XP_011540237.1  non-specific lipid-transfer protein isoform X2

    Conserved Domains (2) summary
    COG0183
    Location:12374
    PaaJ; Acetyl-CoA acetyltransferase [Lipid transport and metabolism]
    cd00826
    Location:17380
    nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
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