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

    Gene ID: 6342, updated on 5-May-2024

    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; AllianceGenome:HGNC:10606
    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; SCOX; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SCP2 in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (52927276..53051698)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (52808787..52933201)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53392948..53517370)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene enoyl-CoA hydratase domain containing 2 Neighboring gene translation machinery-associated protein 7-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53387115-53387797 Neighboring gene ATP synthase membrane subunit j pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53393043-53393558 Neighboring gene H3 histone pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:53440527-53441028 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:53441029-53441528 Neighboring gene RRAS2 pseudogene 1 Neighboring gene tubulin beta class I pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1040 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:53527863-53528050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53546830-53547381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53547382-53547932 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 11 Neighboring gene podocan Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53560558-53561095 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:53571119-53571620 and GRCh37_chr1:53571621-53572120 Neighboring gene solute carrier family 1 member 7 Neighboring gene Sharpr-MPRA regulatory region 13647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53576791-53577515 Neighboring gene uncharacterized LOC105379783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53580852-53581834

    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

    Clone Names

    • DKFZp686C12188, DKFZp686D11188

    Gene Ontology Provided by GOA

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

    General protein information

    Preferred Names
    sterol carrier protein 2
    Names
    SCP-2/3-oxoacyl-CoA thiolase
    SCP-2/thiolase
    acetyl-CoA C-myristoyltransferase
    epididymis secretory sperm binding protein
    non-specific lipid-transfer protein
    propanoyl-CoA C-acyltransferase
    sterol carrier protein X
    straight-chain acyl-CoA oxidase
    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
    XP_047283460.1
    XP_047283462.1
    XP_047283463.1
    XP_047283464.1
    XP_054194110.1
    XP_054194111.1
    XP_054194112.1
    XP_054194113.1
    XP_054194114.1
    XP_054194115.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001007098.3NP_001007099.1  sterol carrier protein 2 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)
      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  sterol carrier protein 2 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  sterol carrier protein 2 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_001007250.3NP_001007251.1  sterol carrier protein 2 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, AL445183, CA867670, M55421
      Consensus CDS
      CCDS30719.1
      UniProtKB/Swiss-Prot
      P22307
      UniProtKB/TrEMBL
      Q59HG9
      Related
      ENSP00000386214.3, ENST00000408941.7
    5. NM_001193599.2NP_001180528.1  sterol carrier protein 2 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/TrEMBL
      B2R761
      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  sterol carrier protein 2 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
      B2R761
      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  sterol carrier protein 2 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/TrEMBL
      B2R761
      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_001330587.2NP_001317516.1  sterol carrier protein 2 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, Q59HG9
      Related
      ENSP00000435194.1, ENST00000478631.6
      Conserved Domains (1) summary
      PRK08256
      Location:12361
      PRK08256; lipid-transfer protein; Provisional
    9. NM_002979.5NP_002970.2  sterol carrier protein 2 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
      A6NM69, B4DGJ9, B4DHP6, C9JC79, D3DQ37, E1B6W5, F2Z3J1, P22307, Q15432, Q16622, Q5VVZ1, Q6NXF4, Q99430
      UniProtKB/TrEMBL
      A0A384NY87, B2R761
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      52927276..53051698
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005271103.5XP_005271160.1  sterol carrier protein 2 isoform X1

      See identical proteins and their annotated locations for XP_005271160.1

      UniProtKB/TrEMBL
      B2R761
      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_047427504.1XP_047283460.1  sterol carrier protein 2 isoform X1

    3. XM_047427507.1XP_047283463.1  sterol carrier protein 2 isoform X2

    4. XM_011541935.3XP_011540237.1  sterol carrier protein 2 isoform X2

      UniProtKB/TrEMBL
      Q59HG9
      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 ...
    5. XM_047427506.1XP_047283462.1  sterol carrier protein 2 isoform X2

    6. XM_047427508.1XP_047283464.1  sterol carrier protein 2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      52808787..52933201
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338136.1XP_054194111.1  sterol carrier protein 2 isoform X1

    2. XM_054338135.1XP_054194110.1  sterol carrier protein 2 isoform X1

    3. XM_054338138.1XP_054194113.1  sterol carrier protein 2 isoform X2

    4. XM_054338139.1XP_054194114.1  sterol carrier protein 2 isoform X2

    5. XM_054338137.1XP_054194112.1  sterol carrier protein 2 isoform X2

    6. XM_054338140.1XP_054194115.1  sterol carrier protein 2 isoform X3