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YJEFN3

gene
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Also known as hYjeF_N3-19p13.11FLJ44968

Summary

YJEFN3 (YjeF N-terminal domain containing 3, HGNC:24785) is a protein-coding gene on chromosome 19p13.11, encoding YjeF N-terminal domain-containing protein 3 (A6XGL0). May accelerate cholesterol efflux from endothelial cells to high-density lipoprotein (HDL) and thereby regulates angiogenesis. It is a selective cancer dependency (DepMap: 12.1% of cell lines).

Predicted to enable NAD(P)HX epimerase activity. Predicted to be involved in several processes, including hematopoietic stem cell proliferation; membrane raft distribution; and negative regulation of angiogenesis. Predicted to be active in mitochondrion.

Source: NCBI Gene 374887 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 62 total
  • Cancer dependency (DepMap): dependent in 12.1% of screened cell lines
  • MANE Select transcript: NM_198537

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24785
Approved symbolYJEFN3
NameYjeF N-terminal domain containing 3
Location19p13.11
Locus typegene with protein product
StatusApproved
AliaseshYjeF_N3-19p13.11, FLJ44968
Ensembl geneENSG00000250067
Ensembl biotypeprotein_coding
OMIM618607
Entrez374887

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 nonsense_mediated_decay

ENST00000436027, ENST00000458210, ENST00000514277, ENST00000877271, ENST00000877272, ENST00000970071, ENST00000970072, ENST00000970073, ENST00000970074, ENST00000970075

RefSeq mRNA: 2 — MANE Select: NM_198537 NM_001190328, NM_198537

CCDS: CCDS42530, CCDS54236

Canonical transcript exons

ENST00000514277 — 7 exons

ExonStartEnd
ENSE000015276001953731919537581
ENSE000020243261952891119528991
ENSE000035083971953533719535450
ENSE000035119971953552919535679
ENSE000036247541952936419529513
ENSE000036261901953503419535144
ENSE000037137211953263219532740

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.50.

FANTOM5 (CAGE): breadth broad, TPM avg 3.0033 / max 244.0114, expressed in 328 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1748061.9536134
1748120.4805161
1748050.233874
1748100.203970
1748110.069027
1748070.062524

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
putamenUBERON:000187498.50gold quality
nucleus accumbensUBERON:000188298.41gold quality
caudate nucleusUBERON:000187398.13gold quality
thymusUBERON:000237097.54gold quality
Ammon’s hornUBERON:000195497.32gold quality
right hemisphere of cerebellumUBERON:001489096.90gold quality
right frontal lobeUBERON:000281096.46gold quality
anterior cingulate cortexUBERON:000983596.31gold quality
temporal lobeUBERON:000187196.29gold quality
amygdalaUBERON:000187696.27gold quality
cerebellar hemisphereUBERON:000224596.12gold quality
superior frontal gyrusUBERON:000266196.10gold quality
cerebellar cortexUBERON:000212996.01gold quality
cerebellumUBERON:000203795.89gold quality
dorsolateral prefrontal cortexUBERON:000983495.79gold quality
Brodmann (1909) area 9UBERON:001354095.78gold quality
cerebral cortexUBERON:000095695.41gold quality
primary visual cortexUBERON:000243695.24gold quality
frontal cortexUBERON:000187095.22gold quality
brainUBERON:000095594.55gold quality
prefrontal cortexUBERON:000045194.41gold quality
right testisUBERON:000453493.67gold quality
left testisUBERON:000453393.10gold quality
hypothalamusUBERON:000189892.73gold quality
testisUBERON:000047391.89gold quality
right uterine tubeUBERON:000130291.54gold quality
sural nerveUBERON:001548891.53gold quality
substantia nigraUBERON:000203890.42gold quality
mucosa of transverse colonUBERON:000499189.85gold quality
cerebellar vermisUBERON:000472087.16gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.33

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.1% of screened cell lines.

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioyjefn3ENSDARG00000061692
mus_musculusYjefn3ENSMUSG00000048967
drosophila_melanogasterNaxeFBGN0030178
caenorhabditis_elegansY18D10A.3WBGENE00012476

Paralogs (1): NAXE (ENSG00000163382)

Protein

Protein identifiers

YjeF N-terminal domain-containing protein 3 — A6XGL0 (reviewed: A6XGL0)

Alternative names: ApoA-I-binding protein 2

All UniProt accessions (2): A6XGL0, A0A087WUA6

UniProt curated annotations — full annotation on UniProt →

Function. May accelerate cholesterol efflux from endothelial cells to high-density lipoprotein (HDL) and thereby regulates angiogenesis. May orchestrate hematopoietic stem and progenitor cell emergence from the hemogenic endothelium, a type of specialized endothelium manifesting hematopoietic potential. YJEFN3-mediated cholesterol efflux activates endothelial SREBF2, the master transcription factor for cholesterol biosynthesis, which in turn transactivates NOTCH and promotes hematopoietic stem and progenitor cell emergence. May play a role in spermiogenesis and oogenesis.

Subunit / interactions. Interacts with APOA1. Binds to HDL.

Tissue specificity. Expressed in theca cells in ovary and in Leydig cells in testis (at protein level). Also expressed in brain and mammary gland.

Isoforms (2)

UniProt IDNamesCanonical?
A6XGL0-11yes
A6XGL0-22

RefSeq proteins (2): NP_001177257, NP_940939* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004443YjeF_N_domDomain
IPR032976YJEFN_prot_NAXE-likeFamily
IPR036652YjeF_N_dom_sfHomologous_superfamily

Pfam: PF03853

UniProt features (5 total): chain 1, domain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A6XGL0-F182.230.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): GOBP_REGULATION_OF_CHOLESTEROL_EFFLUX, GOBP_MEMBRANE_RAFT_ORGANIZATION, GOBP_STEM_CELL_PROLIFERATION, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, GOBP_CHOLESTEROL_EFFLUX, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_SPROUTING_ANGIOGENESIS, GOBP_HEMATOPOIETIC_STEM_CELL_PROLIFERATION, GOBP_BLOOD_VESSEL_MORPHOGENESIS, GOBP_NEGATIVE_REGULATION_OF_VASCULATURE_DEVELOPMENT, GOBP_REGULATION_OF_NOTCH_SIGNALING_PATHWAY, GOBP_REGULATION_OF_STEROL_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_MEMBRANE_ORGANIZATION, GOBP_STEROL_TRANSPORT

GO Biological Process (7): sprouting angiogenesis (GO:0002040), lipid transport (GO:0006869), regulation of Notch signaling pathway (GO:0008593), regulation of cholesterol efflux (GO:0010874), negative regulation of angiogenesis (GO:0016525), membrane raft distribution (GO:0031580), hematopoietic stem cell proliferation (GO:0071425)

GO Molecular Function (2): NAD(P)HX epimerase activity (GO:0052856), protein binding (GO:0005515)

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
angiogenesis2
transport1
lipid localization1
Notch signaling pathway1
regulation of signal transduction1
regulation of cholesterol transport1
cholesterol efflux1
regulation of angiogenesis1
negative regulation of blood vessel morphogenesis1
membrane raft organization1
membrane raft localization1
hemopoiesis1
stem cell proliferation1
racemase and epimerase activity1
binding1
cytoplasm1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

756 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
YJEFN3NAXDQ8IW45549
YJEFN3ZNF101Q8IZC7525
YJEFN3TSSK6Q9BXA6513
YJEFN3ATP13A1Q9HD20478
YJEFN3CILP2Q8IUL8476
YJEFN3GMIPQ9P107475
YJEFN3NDUFA13Q9P0J0452
YJEFN3NOAZFPQ9Y3S2448
YJEFN3ZNF605Q86T29448
YJEFN3OGFOD2Q6N063433
YJEFN3NR2C2APQ86WQ0432
YJEFN3SUGP1Q8IWZ8430
YJEFN3ZNF225Q9UK10419
YJEFN3PBX4Q9BYU1418
YJEFN3GATAD2AQ86YP4418

IntAct

5 interactions, top by confidence:

ABTypeScore
YJEFN3PSMB8psi-mi:“MI:0915”(physical association)0.560
YJEFN3HSPA8psi-mi:“MI:0914”(association)0.350
PSMB8YJEFN3psi-mi:“MI:0915”(physical association)0.000

BioGRID (10): YJEFN3 (Affinity Capture-RNA), YJEFN3 (Affinity Capture-MS), YJEFN3 (Two-hybrid), METTL2B (Affinity Capture-MS), CBWD3 (Affinity Capture-MS), NBEA (Affinity Capture-MS), MAGEE1 (Affinity Capture-MS), UBR3 (Affinity Capture-MS), FEM1B (Affinity Capture-MS), HSPA8 (Affinity Capture-MS)

ESM2 similar proteins: A0JMH2, A5K3F9, A6XGL0, A8IRK7, B0BNM1, B7QDG3, C3YDS7, D3ZEY4, D3ZU57, E2QRY6, E7FCP8, F6W8I0, F7DL67, F7FIH8, O14976, O88444, P16386, P51828, P52333, P52824, P53370, P70563, Q08828, Q0PIT9, Q17QN2, Q2KI13, Q2KI24, Q3TIU4, Q4R4T6, Q5GA22, Q5RAR6, Q5ZHX9, Q6AXQ5, Q6DHK1, Q6L8Q7, Q6P5E8, Q6QRN6, Q8CH40, Q8K2J9, Q8K4Z3

Diamond homologs: A0E3W6, A1S0R2, A4H7T9, A5K3F9, A6XGL0, A7F1E9, A7RPT4, A8BQZ5, A8X5H6, A9A432, B0BNM1, B3L9G8, B3N0Q8, B3NW64, B4GWP5, B4IDM2, B4JJQ3, B4L8C7, B4M2R8, B4NEH6, B4PXF5, B5YIM0, B7QDG3, B8E2P6, B8LCD8, B9KJP6, C0NNH7, C3YDS7, C4M2B8, C4YF50, C7Z508, E0V9D8, E2QRY6, E3KGP2, E3XA68, E9HCD7, F0SLK8, F6W8I0, F7DL67, F7FIH8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance57
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1428 predictions. Top by Δscore:

VariantEffectΔscore
19:19528987:CTCAG:Cdonor_loss1.0000
19:19528988:TCAGG:Tdonor_loss1.0000
19:19528989:CAGG:Cdonor_loss1.0000
19:19528991:GGTC:Gdonor_loss1.0000
19:19528992:G:Cdonor_loss1.0000
19:19532630:A:AGacceptor_gain1.0000
19:19532631:G:GAacceptor_gain1.0000
19:19532631:G:GTacceptor_gain1.0000
19:19532631:GC:Gacceptor_gain1.0000
19:19532631:GCACC:Gacceptor_gain1.0000
19:19532737:CAAG:Cdonor_loss1.0000
19:19532737:CAAGG:Cdonor_loss1.0000
19:19532738:AAG:Adonor_loss1.0000
19:19532739:AGG:Adonor_loss1.0000
19:19532739:AGGT:Adonor_loss1.0000
19:19532740:GGT:Gdonor_loss1.0000
19:19532740:GGTA:Gdonor_loss1.0000
19:19532741:G:GAdonor_loss1.0000
19:19532741:G:GCdonor_loss1.0000
19:19532742:T:Adonor_loss1.0000
19:19535332:CCCA:Cacceptor_loss1.0000
19:19535333:CCA:Cacceptor_loss1.0000
19:19535333:CCAG:Cacceptor_loss1.0000
19:19535334:CAGGA:Cacceptor_loss1.0000
19:19535335:A:AGacceptor_gain1.0000
19:19535335:A:Cacceptor_loss1.0000
19:19535335:A:Tacceptor_loss1.0000
19:19535335:AG:Aacceptor_gain1.0000
19:19535336:G:GAacceptor_gain1.0000
19:19535336:GG:Gacceptor_gain1.0000

AlphaMissense

1898 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:19535661:A:CS226R0.997
19:19535663:C:AS226R0.997
19:19535663:C:GS226R0.997
19:19535125:C:AA137D0.996
19:19535408:C:GC167W0.996
19:19535080:T:AV122D0.995
19:19532712:G:AG97D0.994
19:19532720:A:CS100R0.994
19:19532722:T:AS100R0.994
19:19532722:T:GS100R0.994
19:19532724:C:AA101D0.994
19:19532730:C:AA103D0.994
19:19535353:T:AI149N0.994
19:19535406:T:CC167R0.994
19:19535407:G:AC167Y0.994
19:19535121:T:CC136R0.993
19:19535123:T:GC136W0.993
19:19535112:G:TG133W0.992
19:19535674:C:AP230H0.992
19:19532723:G:CA101P0.991
19:19535122:G:AC136Y0.991
19:19535128:G:CR138P0.991
19:19535134:T:CL140P0.991
19:19535086:G:AC124Y0.989
19:19535087:T:GC124W0.989
19:19535113:G:AG133E0.989
19:19535568:G:CA195P0.989
19:19532681:T:CF87L0.988
19:19532683:T:AF87L0.988
19:19532683:T:GF87L0.988

dbSNP variants (sampled 300 via entrez): RS1000439111 (19:19532223 G>A,C), RS1000471739 (19:19531958 T>C,G), RS1001066110 (19:19534856 G>A,T), RS1001155495 (19:19527760 C>T), RS1001434526 (19:19537832 A>G), RS1001741397 (19:19532736 C>T), RS1001830420 (19:19536738 G>A), RS1001839116 (19:19531349 G>A,C), RS1002151642 (19:19528959 G>A), RS1002156629 (19:19537251 G>C,T), RS1002274065 (19:19528809 C>G,T), RS1002839111 (19:19526991 CAG>C), RS1002938973 (19:19530353 A>G,T), RS1003111560 (19:19536531 T>C), RS1003184931 (19:19536359 C>A)

Disease associations

OMIM: gene MIM:618607 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST002149_11Schizophrenia3.000000e-09
GCST004603_195Platelet count2.000000e-09
GCST006803_88Schizophrenia7.000000e-12
GCST007294_16Body fat distribution (trunk fat ratio)2.000000e-07
GCST007294_35Body fat distribution (trunk fat ratio)1.000000e-10
GCST007295_166Body fat distribution (leg fat ratio)2.000000e-11
GCST007295_22Body fat distribution (leg fat ratio)3.000000e-07
GCST008103_10Bipolar disorder1.000000e-09
GCST008115_2Bipolar I disorder3.000000e-09
GCST008116_4Bipolar II disorder4.000000e-06
GCST010002_52Refractive error4.000000e-29
GCST010703_335Brain morphology (MOSTest)3.000000e-10

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004309platelet count
EFO:0004341body fat distribution
EFO:0009963bipolar I disorder
EFO:0009964bipolar II disorder
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
2,5,2’,5’-tetrachlorobiphenyldecreases expression1
sulforaphaneincreases expression1
manganese chlorideincreases abundance, increases expression1
di-n-butylphosphoric acidaffects expression1
abrineincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Leflunomidedecreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicalsincreases methylation1
Manganeseincreases abundance, increases expression1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1decreases methylation1
Particulate Matterincreases expression, increases abundance1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

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
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot