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STARD3NL

gene
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Also known as MENTHOMGC3251

Summary

STARD3NL (STARD3 N-terminal like, HGNC:19169) is a protein-coding gene on chromosome 7p14.1, encoding STARD3 N-terminal-like protein (O95772). Tethering protein that creates contact site between the endoplasmic reticulum and late endosomes: localizes to late endosome membranes and contacts the endoplasmic reticulum via interaction with VAPA and VAPB.

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).

Source: NCBI Gene 83930 — RefSeq curated summary.

At a glance

  • GWAS associations: 21
  • Clinical variants (ClinVar): 26 total
  • MANE Select transcript: NM_032016

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19169
Approved symbolSTARD3NL
NameSTARD3 N-terminal like
Location7p14.1
Locus typegene with protein product
StatusApproved
AliasesMENTHO, MGC3251
Ensembl geneENSG00000010270
Ensembl biotypeprotein_coding
OMIM611759
Entrez83930

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 35 protein_coding, 1 retained_intron

ENST00000009041, ENST00000396013, ENST00000429075, ENST00000434197, ENST00000440144, ENST00000453225, ENST00000471550, ENST00000881119, ENST00000881120, ENST00000881121, ENST00000881122, ENST00000881123, ENST00000881124, ENST00000881125, ENST00000881126, ENST00000881127, ENST00000881128, ENST00000881129, ENST00000881130, ENST00000919695, ENST00000919696, ENST00000919697, ENST00000919698, ENST00000919699, ENST00000972200, ENST00000972201, ENST00000972202, ENST00000972203, ENST00000972204, ENST00000972205, ENST00000972206, ENST00000972207, ENST00000972208, ENST00000972209, ENST00000972210, ENST00000972211

RefSeq mRNA: 8 — MANE Select: NM_032016 NM_001363339, NM_001363340, NM_001363343, NM_001363344, NM_001363345, NM_001363346, NM_001363347, NM_032016

CCDS: CCDS5455, CCDS87495

Canonical transcript exons

ENST00000009041 — 9 exons

ExonStartEnd
ENSE000006786523821502838215105
ENSE000012358033821702538217078
ENSE000017239833817824538178420
ENSE000018671513822992338230669
ENSE000034833493822879938228871
ENSE000035157843821435738214434
ENSE000035313603821956538219660
ENSE000035954643820744738207729
ENSE000037906933821718838217305

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 98.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.1738 / max 163.1092, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
7820917.89781771
7820814.27591798

Top tissues by expression

261 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065598.52gold quality
oocyteCL:000002397.02gold quality
epithelial cell of pancreasCL:000008396.50gold quality
endothelial cellCL:000011596.11gold quality
ileal mucosaUBERON:000033195.32gold quality
islet of LangerhansUBERON:000000695.26gold quality
ganglionic eminenceUBERON:000402395.20gold quality
embryoUBERON:000092295.19gold quality
hypothalamusUBERON:000189894.79gold quality
C1 segment of cervical spinal cordUBERON:000646994.71gold quality
cortical plateUBERON:000534394.61gold quality
spinal cordUBERON:000224094.54gold quality
ventricular zoneUBERON:000305394.54gold quality
substantia nigraUBERON:000203894.11gold quality
midbrainUBERON:000189193.73gold quality
superior vestibular nucleusUBERON:000722793.69gold quality
monocyteCL:000057693.63gold quality
leukocyteCL:000073893.53gold quality
palpebral conjunctivaUBERON:000181293.38gold quality
adult organismUBERON:000702393.35gold quality
entorhinal cortexUBERON:000272893.23gold quality
amygdalaUBERON:000187693.14gold quality
myocardiumUBERON:000234993.04gold quality
Ammon’s hornUBERON:000195493.03gold quality
tibialis anteriorUBERON:000138592.97silver quality
temporal lobeUBERON:000187192.92gold quality
Brodmann (1909) area 23UBERON:001355492.88gold quality
smooth muscle tissueUBERON:000113592.85gold quality
anterior cingulate cortexUBERON:000983592.85gold quality
placentaUBERON:000198792.77gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-89yes308.46
E-MTAB-6379no399.17
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 6)

  • 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 (PMID:12393907)
  • 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). (PMID:15718238)
  • In this review, MENTHO defines discrete cholesterol-containing subdomains within the membrane of late endosomes where they may function in cholesterol transport. (PMID:16709157)
  • STARD3 or STARD3NL and VAP form a novel molecular tether between late endosomes and the endoplasmic reticulum. (PMID:24105263)
  • STARD3 or STARD3NL-mediated ER-endosome contacts, which affect endosome dynamics, are believed to be involved in cholesterol transport (PMID:27068960)
  • STARD3NL inhibits the osteogenic differentiation by inactivating the Wnt/beta-catenin pathway via binding to Annexin A2 in osteoporosis. (PMID:35098646)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriostard3nlENSDARG00000045421
mus_musculusStard3nlENSMUSG00000003062
rattus_norvegicusStard3nlENSRNOG00000052429
drosophila_melanogasterStart1FBGN0035028
caenorhabditis_elegansWBGENE00010505
caenorhabditis_elegansWBGENE00017826

Paralogs (5): STARD3 (ENSG00000131748), STAR (ENSG00000147465), STARD4 (ENSG00000164211), STARD5 (ENSG00000172345), STARD6 (ENSG00000174448)

Protein

Protein identifiers

STARD3 N-terminal-like protein — O95772 (reviewed: O95772)

Alternative names: MLN64 N-terminal domain homolog

All UniProt accessions (5): O95772, C9J3F5, C9JJ39, C9JKL2, C9JPX5

UniProt curated annotations — full annotation on UniProt →

Function. Tethering protein that creates contact site between the endoplasmic reticulum and late endosomes: localizes to late endosome membranes and contacts the endoplasmic reticulum via interaction with VAPA and VAPB.

Subunit / interactions. Homodimer. Interacts (via the MENTAL domain) with STARD3NL. Interacts (via FFAT motif) with VAPA. Interacts (via FFAT motif) with VAPB. Interacts (via FFAT motif) with MOSPD2 (via MSP domain).

Subcellular location. Late endosome membrane.

Domain organisation. The FFAT motif mediates interaction with VAPA, VAPB and MOSPD2. The MENTAL domain anchors the protein in endosome membranes and exposes the START domain in the cytosol. It binds cholesterol and mediates homotypic as well as heterotypic interactions between STARD3 and STARD3NL.

Similarity. Belongs to the STARD3 family.

Isoforms (2)

UniProt IDNamesCanonical?
O95772-11yes
O95772-22

RefSeq proteins (8): NP_001350268, NP_001350269, NP_001350272, NP_001350273, NP_001350274, NP_001350275, NP_001350276, NP_114405* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019498MENTALDomain
IPR051869STARD3Family

Pfam: PF10457

UniProt features (21 total): topological domain 5, modified residue 5, transmembrane region 4, chain 1, domain 1, region of interest 1, short sequence motif 1, compositionally biased region 1, splice variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95772-F162.780.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 1, 15, 21, 27, 193

Mutagenesis-validated functional residues (1):

PositionPhenotype
209–234loss of interaction with mospd2.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-196108Pregnenolone biosynthesis
R-HSA-1430728Metabolism
R-HSA-196071Metabolism of steroid hormones
R-HSA-556833Metabolism of lipids
R-HSA-8957322Metabolism of steroids

MSigDB gene sets: 151 (showing top): GOBP_VESICLE_LOCALIZATION, GOCC_VACUOLAR_MEMBRANE, ATACCTC_MIR202, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, NKX25_01, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_STEROL_TRANSPORT, GOBP_LIPID_LOCALIZATION, GOBP_ORGANELLE_LOCALIZATION, GOCC_LATE_ENDOSOME_MEMBRANE, GOCC_ORGANELLE_MEMBRANE_CONTACT_SITE, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK

GO Biological Process (2): cholesterol transport (GO:0030301), obsolete vesicle tethering to endoplasmic reticulum (GO:0099044)

GO Molecular Function (3): cholesterol binding (GO:0015485), protein homodimerization activity (GO:0042803), protein binding (GO:0005515)

GO Cellular Component (8): lysosomal membrane (GO:0005765), endosome (GO:0005768), cytosol (GO:0005829), membrane (GO:0016020), late endosome membrane (GO:0031902), organelle membrane contact site (GO:0044232), endoplasmic reticulum-endosome membrane contact site (GO:0140284), endoplasmic reticulum membrane (GO:0005789)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Metabolism of steroid hormones1
Metabolism of steroids1
Metabolism1
Metabolism of lipids1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
sterol transport1
sterol binding1
alcohol binding1
identical protein binding1
protein dimerization activity1
binding1
lysosome1
lytic vacuole membrane1
endomembrane system1
cytoplasmic vesicle1
cytoplasm1
late endosome1
endosome membrane1
organelle1
organelle membrane contact site1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1

Protein interactions and networks

STRING

540 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STARD3NLVAPAQ9P0L0864
STARD3NLNPC2P61916860
STARD3NLSTARP49675787
STARD3NLVAPBO95292766
STARD3NLNPC1O15118755
STARD3NLZFYVE27Q5T4F4604
STARD3NLDCDC1P59894583
STARD3NLMOSPD2Q8NHP6582
STARD3NLSAXO6Q8TC05566
STARD3NLAMPHP49418561
STARD3NLFYCO1Q9BQS8557
STARD3NLZBTB40Q9NUA8545
STARD3NLOR2B3O76000540
STARD3NLEPDR1Q9UM22536
STARD3NLOR10G2Q8NGC3527

IntAct

42 interactions, top by confidence:

ABTypeScore
STARD3NLMOSPD2psi-mi:“MI:0915”(physical association)0.660
STARD3NLMOSPD2psi-mi:“MI:0403”(colocalization)0.660
STARD3NLHCSTpsi-mi:“MI:0915”(physical association)0.560
TNFSF8LGALS8psi-mi:“MI:0914”(association)0.530
STOMEI24psi-mi:“MI:0914”(association)0.510
VAPASTARD3NLpsi-mi:“MI:0403”(colocalization)0.380
VAPASTARD3NLpsi-mi:“MI:2364”(proximity)0.380
STARD3NLCHRM5psi-mi:“MI:0915”(physical association)0.370
STARD3NLELK1psi-mi:“MI:0915”(physical association)0.370
DENND11psi-mi:“MI:0914”(association)0.350
TMEM106BSTX7psi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
STARD3NLAMY1Apsi-mi:“MI:0914”(association)0.350
ATP5PFTMEM120Bpsi-mi:“MI:0914”(association)0.350
ATP5PBSH3PXD2Bpsi-mi:“MI:0914”(association)0.350
GPR35SLC33A1psi-mi:“MI:0914”(association)0.350
LPAR1GOSR2psi-mi:“MI:0914”(association)0.350
LPAR2EI24psi-mi:“MI:0914”(association)0.350
SLC6A5SCAMP3psi-mi:“MI:0914”(association)0.350
GP5MGST3psi-mi:“MI:0914”(association)0.350
KLRC1CLGNpsi-mi:“MI:0914”(association)0.350
P2RY8BTAF1psi-mi:“MI:0914”(association)0.350
STARD3NLGPAA1psi-mi:“MI:0914”(association)0.350
TMEM231WFS1psi-mi:“MI:0914”(association)0.350
ST3GAL1STARD3NLpsi-mi:“MI:0914”(association)0.350
STARD3NLATP5F1Bpsi-mi:“MI:0914”(association)0.350
MFSD5ILVBLpsi-mi:“MI:0914”(association)0.350

BioGRID (63): STOM (Affinity Capture-MS), SYNJ2BP (Co-fractionation), TOMM22 (Co-fractionation), HCST (Two-hybrid), STARD3NL (Affinity Capture-MS), STARD3NL (Proximity Label-MS), STARD3NL (Proximity Label-MS), STARD3NL (Two-hybrid), AMY1C (Affinity Capture-MS), MOSPD2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), CD63 (Affinity Capture-MS), STARD3NL (Affinity Capture-MS), STARD3NL (Affinity Capture-MS), SLC25A4 (Affinity Capture-MS)

ESM2 similar proteins: A4IG66, B2RUZ4, B3DHH5, F1NVK6, F1Q930, O70367, O76024, O77770, O95772, P02683, P0C8K7, P42857, P56695, P84889, Q0P4Z1, Q15053, Q1JPG0, Q28DG6, Q2TBG9, Q4QQM5, Q4R5Q3, Q56JY4, Q5BLE2, Q5M836, Q5RF46, Q5XJS0, Q5ZKK0, Q62092, Q6GR21, Q6IQA2, Q6NRB7, Q6P606, Q7L4E1, Q7Z3D4, Q8BG50, Q8BK03, Q8BXV2, Q8IUW5, Q8K2J7, Q8NAN2

Diamond homologs: F7B909, O46689, O95772, P49675, P51557, P58864, P70114, P79245, P97826, Q14849, Q28918, Q28996, Q61542, Q90ZB9, Q9DCI3, Q9DE06, Q9DEB4, Q9DFS4, Q9DG08, Q9DG09, Q9DG10, Q9W145, A1A4M6, Q5R8P9, Q9EPQ7, Q9NSY2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
SLC-mediated transmembrane transport611.8×7e-04
Transport of small molecules86.7×7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

26 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance16
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1303 predictions. Top by Δscore:

VariantEffectΔscore
7:38178418:AAG:Adonor_loss1.0000
7:38178421:GTAG:Gdonor_loss1.0000
7:38207612:GAT:Gdonor_gain1.0000
7:38207629:G:GTdonor_gain1.0000
7:38207660:G:GTdonor_gain1.0000
7:38214430:TATTT:Tdonor_gain1.0000
7:38214431:ATTT:Adonor_gain1.0000
7:38214432:TTT:Tdonor_gain1.0000
7:38214433:TT:Tdonor_gain1.0000
7:38214435:G:GGdonor_gain1.0000
7:38217172:T:TAacceptor_gain1.0000
7:38217179:A:AGacceptor_gain1.0000
7:38217186:A:AGacceptor_gain1.0000
7:38217187:G:GGacceptor_gain1.0000
7:38217187:GCT:Gacceptor_gain1.0000
7:38217187:GCTT:Gacceptor_gain1.0000
7:38217301:AAACA:Adonor_gain1.0000
7:38217302:AACA:Adonor_gain1.0000
7:38217303:ACA:Adonor_gain1.0000
7:38217303:ACAG:Adonor_loss1.0000
7:38217304:CA:Cdonor_gain1.0000
7:38217305:AG:Adonor_loss1.0000
7:38217306:G:GGdonor_gain1.0000
7:38217307:T:Gdonor_loss1.0000
7:38219561:CCAG:Cacceptor_loss1.0000
7:38219562:CA:Cacceptor_loss1.0000
7:38219563:A:AGacceptor_gain1.0000
7:38219563:A:Cacceptor_loss1.0000
7:38219564:G:GGacceptor_gain1.0000
7:38219564:G:Tacceptor_loss1.0000

AlphaMissense

1526 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:38207685:T:CF61L1.000
7:38207687:T:AF61L1.000
7:38207687:T:GF61L1.000
7:38207712:T:AW70R1.000
7:38207712:T:CW70R1.000
7:38217043:A:CS134R1.000
7:38217045:T:AS134R1.000
7:38217045:T:GS134R1.000
7:38217245:T:AW165R1.000
7:38217245:T:CW165R1.000
7:38207659:G:CR52T0.999
7:38207659:G:TR52M0.999
7:38207660:G:CR52S0.999
7:38207660:G:TR52S0.999
7:38207662:G:TR53M0.999
7:38207663:G:CR53S0.999
7:38207663:G:TR53S0.999
7:38207667:T:CF55L0.999
7:38207669:C:AF55L0.999
7:38207669:C:GF55L0.999
7:38207670:T:CC56R0.999
7:38207674:T:CL57S0.999
7:38207689:A:CD62A0.999
7:38207710:T:CL69P0.999
7:38217222:C:AP157H0.999
7:38217222:C:GP157R0.999
7:38217253:G:CE167D0.999
7:38217253:G:TE167D0.999
7:38217257:T:AW169R0.999
7:38217257:T:CW169R0.999

dbSNP variants (sampled 300 via entrez): RS1000159862 (7:38231061 T>C), RS1000225633 (7:38212773 G>A), RS1000232655 (7:38187849 A>C,G), RS1000356124 (7:38216173 C>T), RS1000437193 (7:38226794 A>G,T), RS1000437780 (7:38181544 A>C), RS1000515915 (7:38200165 A>T), RS1000576000 (7:38193391 T>C), RS1000618826 (7:38207850 C>T), RS1000626236 (7:38202952 T>A,G), RS1000632037 (7:38199755 T>A,G), RS1000681450 (7:38187562 G>A,C), RS1000782353 (7:38220248 A>C), RS1000821146 (7:38214149 A>G), RS1000823858 (7:38214829 G>A)

Disease associations

OMIM: gene MIM:611759 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

21 associations (top):

StudyTraitp-value
GCST000494_5Bone mineral density (spine)1.000000e-09
GCST000817_168Height2.000000e-09
GCST001402_3Treatment response for severe sepsis6.000000e-06
GCST001482_14Lumbar spine bone mineral density4.000000e-38
GCST002647_67Height1.000000e-18
GCST002702_98Height3.000000e-06
GCST004863_94Mosquito bite size9.000000e-06
GCST005790_3Rosacea symptom severity2.000000e-06
GCST006148_8Frontotemporal dementia with GRN mutation6.000000e-06
GCST006288_150Heel bone mineral density4.000000e-28
GCST006288_645Heel bone mineral density6.000000e-57
GCST006288_752Heel bone mineral density2.000000e-28
GCST006423_7Fracture9.000000e-10
GCST006979_348Heel bone mineral density1.000000e-66
GCST006979_349Heel bone mineral density4.000000e-116
GCST006980_7Fracture8.000000e-26
GCST007015_2Lumbar spine bone mineral density (integral)8.000000e-07
GCST008839_149Height3.000000e-14
GCST009115_4Heel bone mineral density variance2.000000e-13
GCST009120_4Heel bone mineral density3.000000e-86
GCST010242_226HDL cholesterol levels9.000000e-09

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0008378mosquito bite reaction size measurement
EFO:0009180rosacea severity measurement
EFO:0009270heel bone mineral density
EFO:0007620volumetric bone mineral density
EFO:0004612high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
FR900359increases phosphorylation1
alpha phellandreneincreases expression1
bisphenol Aincreases methylation, affects cotreatment1
arseniteaffects binding, increases reaction1
benzo(e)pyreneincreases methylation1
coumarinincreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
ICG 001decreases expression1
bisphenol Sincreases methylation1
Resveratrolaffects cotreatment, increases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Caffeinedecreases phosphorylation1
Doxorubicinaffects expression1
Leadaffects splicing1
Methapyrileneincreases methylation1
Phenobarbitalaffects expression1
Phthalic Acidsdecreases methylation1
Plant Extractsaffects cotreatment, increases expression1
Tetrachlorodibenzodioxindecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Aflatoxin B1decreases methylation1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): bone fracture, frontotemporal dementia

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
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BioBTree
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Sources 75

This page pulls from 75 datasets indexed by BioBTree:

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