STARD4

gene
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Summary

STARD4 (StAR related lipid transfer domain containing 4, HGNC:18058) is a protein-coding gene on chromosome 5q22.1, encoding StAR-related lipid transfer protein 4 (Q96DR4). Involved in the intracellular transport of cholesterol.

Cholesterol homeostasis is regulated, at least in part, by sterol regulatory element (SRE)-binding proteins (e.g., SREBP1; MIM 184756) and by liver X receptors (e.g., LXRA; MIM 602423). Upon sterol depletion, LXRs are inactive and SREBPs are cleaved, after which they bind promoter SREs and activate genes involved in cholesterol biosynthesis and uptake. Sterol transport is mediated by vesicles or by soluble protein carriers, such as steroidogenic acute regulatory protein (STAR; MIM 600617). STAR is homologous to a family of proteins containing a 200- to 210-amino acid STAR-related lipid transfer (START) domain, including STARD4 (Soccio et al., 2002 [PubMed 12011452]).

Source: NCBI Gene 134429 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 26 total
  • MANE Select transcript: NM_139164

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18058
Approved symbolSTARD4
NameStAR related lipid transfer domain containing 4
Location5q22.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000164211
Ensembl biotypeprotein_coding
OMIM607049
Entrez134429

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 12 protein_coding, 4 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000296632, ENST00000455172, ENST00000502322, ENST00000502931, ENST00000505803, ENST00000508215, ENST00000509887, ENST00000510346, ENST00000511137, ENST00000511436, ENST00000511569, ENST00000512160, ENST00000925892, ENST00000925893, ENST00000925894, ENST00000925895, ENST00000925896, ENST00000925897, ENST00000954329

RefSeq mRNA: 7 — MANE Select: NM_139164 NM_001308056, NM_001308057, NM_001308058, NM_001308059, NM_001308060, NM_001308061, NM_139164

CCDS: CCDS4104, CCDS78046

Canonical transcript exons

ENST00000296632 — 6 exons

ExonStartEnd
ENSE00001263084111496033111500106
ENSE00002080404111512385111512535
ENSE00003467152111501962111502088
ENSE00003494506111501002111501116
ENSE00003497181111507329111507442
ENSE00003590177111506330111506379

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 97.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.5075 / max 6108.2068, expressed in 1810 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
6291733.57731801
629152.69991150
629161.8296928
629181.53371009
629190.8670104

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
adrenal tissueUBERON:001830397.45gold quality
ileal mucosaUBERON:000033197.04gold quality
jejunal mucosaUBERON:000039991.94gold quality
duodenumUBERON:000211489.73gold quality
right hemisphere of cerebellumUBERON:001489088.57gold quality
rectumUBERON:000105288.17gold quality
right lungUBERON:000216788.14gold quality
vermiform appendixUBERON:000115488.06gold quality
cerebellar cortexUBERON:000212987.74gold quality
cerebellar hemisphereUBERON:000224587.71gold quality
islet of LangerhansUBERON:000000687.62gold quality
upper lobe of left lungUBERON:000895287.45gold quality
cerebellumUBERON:000203787.33gold quality
upper lobe of lungUBERON:000894887.23gold quality
pancreatic ductal cellCL:000207987.22gold quality
C1 segment of cervical spinal cordUBERON:000646987.19gold quality
prefrontal cortexUBERON:000045186.91gold quality
lungUBERON:000204886.84gold quality
ventricular zoneUBERON:000305386.70gold quality
cerebellar vermisUBERON:000472086.27silver quality
pigmented layer of retinaUBERON:000178286.17gold quality
spinal cordUBERON:000224086.07gold quality
Brodmann (1909) area 9UBERON:001354085.90gold quality
popliteal arteryUBERON:000225085.89gold quality
tibial arteryUBERON:000761085.89gold quality
placentaUBERON:000198785.66gold quality
dorsolateral prefrontal cortexUBERON:000983485.35gold quality
embryoUBERON:000092285.31gold quality
ganglionic eminenceUBERON:000402385.31gold quality
cartilage tissueUBERON:000241885.26gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes12.18
E-GEOD-75140no251.69

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF6, SREBF2

miRNA regulators (miRDB)

177 targeting STARD4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4262100.0073.263931
HSA-MIR-3163100.0077.238605
HSA-MIR-126-5P100.0072.713180
HSA-MIR-1252-5P100.0069.802774
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-4795-3P100.0074.624024
HSA-LET-7A-3P100.0074.033932
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-5692A100.0074.406850
HSA-MIR-366299.9973.825684
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-450099.9972.722367
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-477599.9875.006394
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790

Literature-anchored findings (GeneRIF, showing 16)

  • StarD4 is regulated by sterols via SREBP-2, and StarD5 is activated by ER stress cholesterol metabolism; they serve different functions (PMID:15760897)
  • Induction of STARD4 depended on both transcription factor ATF6 and an ERSE-like element in its promoter. (PMID:16579971)
  • StarD4 plays an important role as a directional cholesterol transporter in the maintenance of cellular cholesterol homeostasis (PMID:18403318)
  • StarD4-accelerated 7 alpha-OOH transfer to mitochondria resulted in greater susceptibility to free radical lipid peroxidation and loss of membrane potential than in a non-StarD4 control. (PMID:20059974)
  • Study provide strong evidence for StarD4 as a highly regulated, non-vesicular, directional, intracellular transporter of cholesterol which plays a key role in the maintenance of intracellular cholesterol homeostasis. (PMID:21767660)
  • cholesterol transport mediated by STARD4 is an important component of the cholesterol homeostasis regulatory machinery (PMID:21900492)
  • The data indicate a role for STARD4 in nonvesicular transport of cholesterol from the plasma membrane and the endocytic recycling compartment to the endoplasmic reticulum and perhaps other intracellular compartments as well. (PMID:23033213)
  • Studies show the 3 steroidogenic acute regulatory-related lipid transfer (START) domain proteins StarD4, StarD5 and StarD6 have a similar lipid binding pocket specific for sterols (cholesterol in particular), but differing regulation and localization. (PMID:24440759)
  • This study shows that nonvesicular sterol transport mechanisms and STARD4 in particular account for a large fraction of sterol transport between the plasma membrane and the ERC. (PMID:28209730)
  • STARD4 has a conserved alpha-helix/beta-grip fold with a deep hydrophobic pocket.STARD4 binds sterol in the pocket and transport sterol between liposomes. Sterol binding requires a conformational change to form a complementary pocket. (PMID:31607485)
  • Knockdown of STARD4, a sterol transporter, leads to large changes in the lipidome. STARD4-KD cells also have large changes in their mRNA profile. There is an increase in cellular cholesterol, including in late endosomes. These results indicate that STARD4 plays important roles in lipid homeostasis. (PMID:31917335)
  • STARD4 promotes breast cancer cell malignancy. (PMID:33125124)
  • [Steroidogenic acute regulatory protein-related lipid transfer 4 (StarD4) promotes breast cancer cell proliferation and its mechanism]. (PMID:34970895)
  • SREBF2-STARD4 axis confers sorafenib resistance in hepatocellular carcinoma by regulating mitochondrial cholesterol homeostasis. (PMID:35642354)
  • Membrane specificity of the human cholesterol transfer protein STARD4. (PMID:38615744)
  • Differential regulation of STARD1, STARD4 and STARD6 in the human ovary. (PMID:38829257)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriostard4ENSDARG00000102477
mus_musculusStard4ENSMUSG00000024378
rattus_norvegicusStard4ENSRNOG00000020468
drosophila_melanogasterStart1FBGN0035028
caenorhabditis_elegansWBGENE00010505
caenorhabditis_elegansWBGENE00017826

Paralogs (5): STARD3NL (ENSG00000010270), STARD3 (ENSG00000131748), STAR (ENSG00000147465), STARD5 (ENSG00000172345), STARD6 (ENSG00000174448)

Protein

Protein identifiers

StAR-related lipid transfer protein 4Q96DR4 (reviewed: Q96DR4)

Alternative names: START domain-containing protein 4

All UniProt accessions (3): D6RDM5, D6REN7, Q96DR4

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the intracellular transport of cholesterol. Binds cholesterol or other sterols.

Isoforms (2)

UniProt IDNamesCanonical?
Q96DR4-11yes
Q96DR4-22

RefSeq proteins (7): NP_001294985, NP_001294986, NP_001294987, NP_001294988, NP_001294989, NP_001294990, NP_631903* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002913START_lipid-bd_domDomain
IPR023393START-like_dom_sfHomologous_superfamily
IPR042555StarD4Family

Pfam: PF01852

Catalyzed reactions (Rhea), 1 shown:

  • cholesterol(in) = cholesterol(out) (RHEA:39747)

UniProt features (20 total): strand 11, helix 5, chain 1, domain 1, turn 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6L1MX-RAY DIFFRACTION1.7
6L1DX-RAY DIFFRACTION1.95

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96DR4-F196.030.96

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: 276 (showing top): RNGTGGGC_UNKNOWN, MODULE_97, CCAWYNNGAAR_UNKNOWN, MENSE_HYPOXIA_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MODULE_182, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_KETONE_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, GOBP_BILE_ACID_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS

GO Biological Process (6): cholesterol transport involved in cholesterol storage (GO:0010879), intracellular cholesterol transport (GO:0032367), cholesterol import (GO:0070508), positive regulation of bile acid biosynthetic process (GO:0070859), positive regulation of cholesterol metabolic process (GO:0090205), lipid transport (GO:0006869)

GO Molecular Function (4): cholesterol binding (GO:0015485), cholesterol transfer activity (GO:0120020), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (4): cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), cytoplasmic vesicle (GO:0031410)

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
cholesterol transport3
cytoplasm3
intracellular anatomical structure2
positive regulation of small molecule metabolic process2
binding2
cellular anatomical structure2
lipid transport involved in lipid storage1
cholesterol storage1
intracellular sterol transport1
bile acid biosynthetic process1
positive regulation of steroid biosynthetic process1
regulation of bile acid biosynthetic process1
cholesterol metabolic process1
positive regulation of steroid metabolic process1
regulation of cholesterol metabolic process1
transport1
lipid localization1
sterol binding1
alcohol binding1
cholesterol binding1
sterol transfer activity1
endomembrane system1
intracellular membrane-bounded organelle1
intracellular vesicle1

Protein interactions and networks

STRING

586 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STARD4PCTPQ9UKL6940
STARD4SREBF1P36956656
STARD4CERT1Q9Y5P4647
STARD4NR1H3Q13133568
STARD4STARD3Q14849557
STARD4HMGCS1Q01581525
STARD4OSBPP22059499
STARD4NPC1O15118488
STARD4STARD10Q9Y365488
STARD4SREBF2Q12772480
STARD4STARD7Q9NQZ5478
STARD4MSMO1Q15800475
STARD4DGLUCYQ7Z3D6469
STARD4HMGCRP04035466
STARD4SQLEQ14534463

IntAct

19 interactions, top by confidence:

ABTypeScore
ARL6IP1STARD4psi-mi:“MI:0915”(physical association)0.560
CCHCR1STARD4psi-mi:“MI:0915”(physical association)0.560
AGTRAPSTARD4psi-mi:“MI:0915”(physical association)0.560
GDAP1STARD4psi-mi:“MI:0915”(physical association)0.560
STARD4MTIF3psi-mi:“MI:0915”(physical association)0.560
SYPSTARD4psi-mi:“MI:0915”(physical association)0.560
STARD4AGTRAPpsi-mi:“MI:0915”(physical association)0.000
STARD4ARL6IP1psi-mi:“MI:0915”(physical association)0.000
STARD4CCHCR1psi-mi:“MI:0915”(physical association)0.000
STARD4GDAP1psi-mi:“MI:0915”(physical association)0.000
STARD4SYPpsi-mi:“MI:0915”(physical association)0.000
STARD4MTIF3psi-mi:“MI:0915”(physical association)0.000

BioGRID (8): STARD4 (Two-hybrid), STARD4 (Two-hybrid), STARD4 (Two-hybrid), ARL6IP1 (Two-hybrid), AGTRAP (Two-hybrid), CCHCR1 (Two-hybrid), STARD4 (Affinity Capture-RNA), STARD4 (Affinity Capture-RNA)

ESM2 similar proteins: A1A4M6, A5GFX0, A5PJU6, O46689, O88736, P49675, P51557, P53808, P59095, P59096, P70114, P79245, P97826, Q28918, Q28996, Q3U1V6, Q4R5S9, Q58DB0, Q5BKH5, Q5IH13, Q5IH14, Q5R8P9, Q64421, Q6GM21, Q6IQS6, Q6NTS7, Q6P9U4, Q6TMK8, Q8R1R3, Q8VE85, Q8WYK0, Q90673, Q90ZB9, Q94E75, Q96DR4, Q96N28, Q99JV5, Q99NB7, Q9CYY7, Q9DBK0

Diamond homologs: A1A4M6, P59095, P59096, Q5R8P9, Q96DR4, Q99JV5, Q9EPQ7, Q9NSY2, Q61542

SIGNOR signaling

0 interactions.

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 significance23
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1104 predictions. Top by Δscore:

VariantEffectΔscore
5:111501112:CAATT:Cacceptor_gain1.0000
5:111501113:AATT:Aacceptor_gain1.0000
5:111501114:ATTC:Aacceptor_loss1.0000
5:111501115:TT:Tacceptor_gain1.0000
5:111501115:TTCT:Tacceptor_loss1.0000
5:111501116:TCTG:Tacceptor_loss1.0000
5:111501117:C:CCacceptor_gain1.0000
5:111501117:C:Tacceptor_loss1.0000
5:111501118:T:Cacceptor_loss1.0000
5:111501957:GATAC:Gdonor_loss1.0000
5:111501958:ATACC:Adonor_loss1.0000
5:111501959:TACC:Tdonor_loss1.0000
5:111501960:A:Tdonor_loss1.0000
5:111501961:C:Gdonor_loss1.0000
5:111502089:C:CCacceptor_gain1.0000
5:111506328:A:ACdonor_gain1.0000
5:111506329:C:CCdonor_gain1.0000
5:111499860:C:CTdonor_gain0.9900
5:111499861:T:TTdonor_gain0.9900
5:111499932:G:Adonor_gain0.9900
5:111501019:T:TAdonor_gain0.9900
5:111501114:ATT:Aacceptor_gain0.9900
5:111501961:CCT:Cdonor_gain0.9900
5:111501963:T:TAdonor_gain0.9900
5:111502084:TGTAG:Tacceptor_gain0.9900
5:111502086:TAG:Tacceptor_gain0.9900
5:111502087:AG:Aacceptor_gain0.9900
5:111502088:GC:Gacceptor_loss0.9900
5:111502089:C:Tacceptor_loss0.9900
5:111502090:T:Aacceptor_loss0.9900

AlphaMissense

1355 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:111501051:A:CF116L0.998
5:111501051:A:TF116L0.998
5:111501053:A:GF116L0.998
5:111499938:G:TA189D0.996
5:111500041:A:GW155R0.996
5:111500041:A:TW155R0.996
5:111501057:T:AR114S0.996
5:111501057:T:GR114S0.996
5:111502009:A:GW79R0.996
5:111502009:A:TW79R0.996
5:111507349:A:GW29R0.996
5:111507349:A:TW29R0.996
5:111500043:C:TG154D0.995
5:111500099:A:CS135R0.995
5:111500099:A:TS135R0.995
5:111500101:T:GS135R0.995
5:111501052:A:GF116S0.994
5:111501067:A:TI111N0.994
5:111502007:C:AW79C0.994
5:111502007:C:GW79C0.994
5:111502018:G:TR76S0.994
5:111500061:C:TG148E0.993
5:111502006:C:GD80H0.993
5:111501047:C:GD118H0.992
5:111501052:A:CF116C0.992
5:111501058:C:GR114T0.992
5:111502005:T:GD80A0.992
5:111499939:C:GA189P0.991
5:111502005:T:AD80V0.991
5:111499990:A:CY172D0.990

dbSNP variants (sampled 300 via entrez): RS1000181162 (5:111502580 G>C), RS1000232732 (5:111505809 A>C,G), RS1000365692 (5:111498021 A>G,T), RS1000735976 (5:111496640 C>G,T), RS1000842576 (5:111499756 G>A), RS1000872074 (5:111506396 A>C), RS1001106205 (5:111496317 A>G), RS1001241321 (5:111499664 CAGAGTG>C), RS1001399677 (5:111500013 G>C), RS1001477641 (5:111505859 A>G), RS1001487845 (5:111509804 G>A), RS1001678502 (5:111512685 A>C), RS1001772245 (5:111499672 G>A,C), RS1001886607 (5:111504642 A>T), RS1002093855 (5:111511942 G>C)

Disease associations

OMIM: gene MIM:607049 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST002541_14Menarche (age at onset)3.000000e-10
GCST002875_171Diisocyanate-induced asthma2.000000e-06
GCST007507_8Benign prostatic hyperplasia and lower urinary tract symptoms4.000000e-12
GCST009798_4Asthma1.000000e-14
GCST009798_60Asthma1.000000e-44
GCST010320_81PR interval3.000000e-09
GCST010321_2PR interval5.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004703age at menarche
EFO:0006995response to diisocyanate
EFO:0008008lower urinary tract symptom
EFO:0004462PR interval

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

55 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression3
methylmercuric chloridedecreases expression2
Resveratrolincreases expression, affects cotreatment2
Arsenic Trioxideaffects cotreatment, decreases expression2
Arsenicaffects methylation, affects cotreatment, decreases expression, increases abundance2
Valproic Aciddecreases expression, decreases methylation2
aristolochic acid Idecreases expression1
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amineincreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
trichostatin Aaffects expression1
dodecyldimethylamine oxideincreases expression1
beta-lapachonedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
cupric chloridedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
dinophysistoxin 1decreases expression1
yessotoxinincreases expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
monomethylarsonous aciddecreases expression1
azaspiracidincreases expression1
ICG 001decreases expression1
abrinedecreases expression1
jinfukangaffects cotreatment, increases expression1
PP242decreases expression1
Dasatinibaffects cotreatment, decreases expression1
Decitabinedecreases expression, decreases reaction1
Air Pollutantsdecreases 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): benign prostatic hyperplasia