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    STARD3NL STARD3 N-terminal like [ Homo sapiens (human) ]

    Gene ID: 83930, updated on 3-Nov-2024

    Summary

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    Official Symbol
    STARD3NLprovided by HGNC
    Official Full Name
    STARD3 N-terminal likeprovided by HGNC
    Primary source
    HGNC:HGNC:19169
    See related
    Ensembl:ENSG00000010270 MIM:611759; AllianceGenome:HGNC:19169
    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
    MENTHO
    Summary
    This gene encodes a late-endosomal protein that contains a conserved MENTAL (MLN64 N-terminal) domain. The encoded protein binds cholesterol molecules and may play a role in endosomal cholesterol transport through interactions with metastatic lymph node protein 64 (MLN64). [provided by RefSeq, Sep 2011]
    Expression
    Ubiquitous expression in prostate (RPKM 17.0), placenta (RPKM 15.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See STARD3NL in Genome Data Viewer
    Location:
    7p14.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (38178245..38230669)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (38319177..38371581)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (38217847..38270270)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18107 Neighboring gene Sharpr-MPRA regulatory region 10360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987061-37987582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987583-37988102 Neighboring gene ependymin related 1 Neighboring gene Sharpr-MPRA regulatory region 4879 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38026488-38027240 Neighboring gene MPRA-validated peak6491 silencer Neighboring gene uncharacterized LOC105375236 Neighboring gene MPRA-validated peak6492 silencer Neighboring gene MPRA-validated peak6493 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38110217-38110835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18108 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:38214547-38215746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18109 Neighboring gene Sharpr-MPRA regulatory region 13548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25866 Neighboring gene MPRA-validated peak6494 silencer Neighboring gene T cell receptor gamma constant 2 Neighboring gene T cell receptor gamma locus Neighboring gene T cell receptor gamma joining 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. STARD3NL inhibits the osteogenic differentiation by inactivating the Wnt/beta-catenin pathway via binding to Annexin A2 in osteoporosis.
      Title: STARD3NL inhibits the osteogenic differentiation by inactivating the Wnt/β-catenin pathway via binding to Annexin A2 in osteoporosis.
    2. STARD3 or STARD3NL-mediated ER-endosome contacts, which affect endosome dynamics, are believed to be involved in cholesterol transport
      Title: Touché! STARD3 and STARD3NL tether the ER to endosomes.
    3. STARD3 or STARD3NL and VAP form a novel molecular tether between late endosomes and the endoplasmic reticulum.
      Title: STARD3 or STARD3NL and VAP form a novel molecular tether between late endosomes and the ER.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    6. In this review, MENTHO defines discrete cholesterol-containing subdomains within the membrane of late endosomes where they may function in cholesterol transport.
      Title: MLN64 and MENTHO, two mediators of endosomal cholesterol transport.
    7. The MENTAL (MLN64 amino-terminal shared with MENTHO) domain might serve to maintain cholesterol at the membrane of late endosomes prior to its shuttle to cytoplasmic acceptor(s).
      Title: Functional characterization of the MENTAL domain.
    8. overexpression does not rescue the Niemann-Pick type C lipid storage phenotype; overexpression alters severely the endocytic compartment by leading at steady state to the accumulation of enlarged endosomes
      Title: MENTHO, a MLN64 homologue devoid of the START domain.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Beyond single-marker analyses: mining whole genome scans for insights into treatment responses in severe sepsis.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog
    Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of STARD3 N-terminal like (STARD3NL) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC3251

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cholesterol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cholesterol binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cholesterol transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle tethering to endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle tethering to endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    colocalizes_with endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum-endosome membrane contact site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum-endosome membrane contact site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal membrane HDA PubMed 
    located_in membrane HDA PubMed 
    located_in organelle membrane contact site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    STARD3 N-terminal-like protein
    Names
    MLN64 N-terminal domain homolog

    NCBI Reference Sequences (RefSeq)

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    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_030015.2 RefSeqGene

      Range
      5002..57426
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001363339.2 → NP_001350268.1  STARD3 N-terminal-like protein isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC006033, AJ492267, BQ716734, DT218211
      Consensus CDS
      CCDS5455.1
      UniProtKB/Swiss-Prot
      A4D1X0, O95772
      UniProtKB/TrEMBL
      C9JPX5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 212
      MENTAL; Cholesterol-capturing domain

    2. NM_001363340.2 → NP_001350269.1  STARD3 N-terminal-like protein isoform 1

      Status: REVIEWED

      Source sequence(s)
      AJ492267, BQ716734, DA258701, DT218211
      Consensus CDS
      CCDS5455.1
      UniProtKB/Swiss-Prot
      A4D1X0, O95772
      UniProtKB/TrEMBL
      C9JPX5
      Related
      ENSP00000379334.1, ENST00000396013.5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 212
      MENTAL; Cholesterol-capturing domain

    3. NM_001363343.2 → NP_001350272.1  STARD3 N-terminal-like protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC006033, AJ492267, DT218211
      Consensus CDS
      CCDS87495.1
      UniProtKB/TrEMBL
      C9JKL2, C9JPX5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 194
      MENTAL; Cholesterol-capturing domain

    4. NM_001363344.2 → NP_001350273.1  STARD3 N-terminal-like protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AJ492267, DA258701, DT218211
      Consensus CDS
      CCDS87495.1
      UniProtKB/TrEMBL
      C9JKL2, C9JPX5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 194
      MENTAL; Cholesterol-capturing domain

    5. NM_001363345.2 → NP_001350274.1  STARD3 N-terminal-like protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AJ492267, DA131127
      Consensus CDS
      CCDS87495.1
      UniProtKB/TrEMBL
      C9JKL2, C9JPX5
      Related
      ENSP00000394000.1, ENST00000434197.5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 194
      MENTAL; Cholesterol-capturing domain

    6. NM_001363346.2 → NP_001350275.1  STARD3 N-terminal-like protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC006033, AJ492267, DT218211
      Consensus CDS
      CCDS87495.1
      UniProtKB/TrEMBL
      C9JKL2, C9JPX5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 194
      MENTAL; Cholesterol-capturing domain

    7. NM_001363347.2 → NP_001350276.1  STARD3 N-terminal-like protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC006033, AC093460
      Consensus CDS
      CCDS87495.1
      UniProtKB/TrEMBL
      C9JKL2, C9JPX5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 194
      MENTAL; Cholesterol-capturing domain

    8. NM_032016.4 → NP_114405.1  STARD3 N-terminal-like protein isoform 1

      See identical proteins and their annotated locations for NP_114405.1

      Status: REVIEWED

      Source sequence(s)
      AJ492267, DT218211
      Consensus CDS
      CCDS5455.1
      UniProtKB/Swiss-Prot
      A4D1X0, O95772
      UniProtKB/TrEMBL
      C9JPX5
      Related
      ENSP00000009041.7, ENST00000009041.12
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 212
      MENTAL; Cholesterol-capturing domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      38178245..38230669
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011515572.2 → XP_011513874.1  STARD3 N-terminal-like protein isoform X1

      See identical proteins and their annotated locations for XP_011513874.1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772
      UniProtKB/TrEMBL
      C9JPX5
      Related
      ENSP00000402028.1, ENST00000429075.1
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 212
      MENTAL; Cholesterol-capturing domain

    2. XM_047420921.1 → XP_047276877.1  STARD3 N-terminal-like protein isoform X2

      UniProtKB/TrEMBL
      C9JKL2

    3. XM_047420920.1 → XP_047276876.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772

    4. XM_017012693.2 → XP_016868182.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772
      UniProtKB/TrEMBL
      C9JPX5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 212
      MENTAL; Cholesterol-capturing domain

    5. XM_024446955.2 → XP_024302723.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772
      UniProtKB/TrEMBL
      C9JPX5
      Conserved Domains (1) summary
      pfam10457
      Location:49 → 212
      MENTAL; Cholesterol-capturing domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      38319177..38371581
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359174.1 → XP_054215149.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772

    2. XM_054359175.1 → XP_054215150.1  STARD3 N-terminal-like protein isoform X2

      UniProtKB/TrEMBL
      C9JKL2

    3. XM_054359171.1 → XP_054215146.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772

    4. XM_054359170.1 → XP_054215145.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772

    5. XM_054359172.1 → XP_054215147.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772

    6. XM_054359173.1 → XP_054215148.1  STARD3 N-terminal-like protein isoform X1

      UniProtKB/Swiss-Prot
      A4D1X0, O95772
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95772.1 GenPept UniProtKB/Swiss-Prot:O95772

    Gene LinkOut

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