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

Gene ID: 83930, updated on 3-Apr-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
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Genomic context

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Location:
7p14.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (38178245..38230669)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (38319177..38371581)
105.20220307 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
  • 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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Related articles in PubMed

  1. Touché! STARD3 and STARD3NL tether the ER to endosomes. Wilhelm LP, et al. Biochem Soc Trans, 2016 Apr 15. PMID 27068960
  2. MLN64 and MENTHO, two mediators of endosomal cholesterol transport. Alpy F, et al. Biochem Soc Trans, 2006 Jun. PMID 16709157
  3. MENTHO, a MLN64 homologue devoid of the START domain. Alpy F, et al. J Biol Chem, 2002 Dec 27. PMID 12393907
  4. STARD3NL inhibits the osteogenic differentiation by inactivating the Wnt/β-catenin pathway via binding to Annexin A2 in osteoporosis. Xu Y, et al. J Cell Mol Med, 2022 Mar. PMID 35098646, Free PMC Article
  5. Functional characterization of the MENTAL domain. Alpy F, et al. J Biol Chem, 2005 May 6. PMID 15718238

See all (38) citations in PubMed

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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

Genotypes

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_2023_10

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

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