UNC5D

gene
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Also known as KIAA1777Unc5h4

Summary

UNC5D (unc-5 netrin receptor D, HGNC:18634) is a protein-coding gene on chromosome 8p12, encoding Netrin receptor UNC5D (Q6UXZ4). Receptor for the netrin NTN4 that promotes neuronal cell survival.

Predicted to enable netrin receptor activity. Involved in cell-cell adhesion via plasma-membrane adhesion molecules. Predicted to be located in cell surface and plasma membrane.

Source: NCBI Gene 137970 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 92 total
  • MANE Select transcript: NM_080872

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18634
Approved symbolUNC5D
Nameunc-5 netrin receptor D
Location8p12
Locus typegene with protein product
StatusApproved
AliasesKIAA1777, Unc5h4
Ensembl geneENSG00000156687
Ensembl biotypeprotein_coding
OMIM616466
Entrez137970

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 retained_intron

ENST00000287272, ENST00000404895, ENST00000416672, ENST00000420357, ENST00000449677, ENST00000453357, ENST00000474634

RefSeq mRNA: 3 — MANE Select: NM_080872 NM_001322818, NM_001410918, NM_080872

CCDS: CCDS6093, CCDS83279, CCDS94280

Canonical transcript exons

ENST00000404895 — 17 exons

ExonStartEnd
ENSE000008907693559555435595657
ENSE000010278063556809835568241
ENSE000010278163568354735683727
ENSE000010278203576690235767066
ENSE000010278213575058235750809
ENSE000010278243573101235731096
ENSE000010278273577429935774477
ENSE000010278293574852735748695
ENSE000010278303575932035759469
ENSE000010894453572615235726529
ENSE000011567063570592935705961
ENSE000011567243554929235549510
ENSE000015510723579035935796540
ENSE000017325503523547535235887
ENSE000035301783572221035722395
ENSE000035826593568654535686709
ENSE000036279153568458235684749

Expression profiles

Bgee: expression breadth ubiquitous, 117 present calls, max score 95.25.

FANTOM5 (CAGE): breadth broad, TPM avg 3.7820 / max 175.5400, expressed in 373 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
884013.2037353
884000.4375189
884020.140882

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
embryoUBERON:000092295.25gold quality
ganglionic eminenceUBERON:000402395.25gold quality
endothelial cellCL:000011592.95gold quality
Brodmann (1909) area 23UBERON:001355490.19gold quality
middle temporal gyrusUBERON:000277188.18gold quality
cortical plateUBERON:000534384.92gold quality
primary visual cortexUBERON:000243681.70gold quality
Brodmann (1909) area 46UBERON:000648381.14gold quality
entorhinal cortexUBERON:000272880.92gold quality
buccal mucosa cellCL:000233680.81silver quality
occipital lobeUBERON:000202180.80gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.36gold quality
superior frontal gyrusUBERON:000266180.32gold quality
parietal lobeUBERON:000187277.81gold quality
duodenumUBERON:000211477.56gold quality
postcentral gyrusUBERON:000258177.46gold quality
prefrontal cortexUBERON:000045175.74gold quality
jejunal mucosaUBERON:000039975.20gold quality
frontal cortexUBERON:000187074.71gold quality
ventricular zoneUBERON:000305374.62gold quality
neocortexUBERON:000195073.72gold quality
dorsolateral prefrontal cortexUBERON:000983473.66gold quality
islet of LangerhansUBERON:000000673.28gold quality
cerebral cortexUBERON:000095672.52gold quality
Brodmann (1909) area 9UBERON:001354072.09gold quality
temporal lobeUBERON:000187171.02gold quality
superior vestibular nucleusUBERON:000722770.40gold quality
ileal mucosaUBERON:000033169.59gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099169.40gold quality
jejunumUBERON:000211569.03gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-25yes1393.46
E-GEOD-75140yes594.41
E-HCAD-35yes71.45
E-ANND-3yes7.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

350 targeting UNC5D, 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-3646100.0073.565283
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4262100.0073.263931
HSA-MIR-3163100.0077.238605
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-4682100.0068.891258
HSA-MIR-4481100.0066.421669
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-126-5P100.0072.713180
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-5692A100.0074.406850
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-9-5P100.0072.282361
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3924100.0072.092394
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
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-366299.9973.825684

Literature-anchored findings (GeneRIF, showing 9)

  • UNC5H4 amplifies p53-dependent apoptotic response. (PMID:18402767)
  • UNC5D is a functional tumor suppressor that is frequently downregulated in RCCs due to promoter hypermethylation and LOH. (PMID:23589179)
  • UNC5D forms a positive feedback loop with p53 and E2F1 to promote NGF dependence-mediated programmed cell death during neuroblastoma regression. (PMID:23778138)
  • the dependence receptor UNC5H4 may act as a putative tumor suppressor in neuroblastoma. (PMID:24519068)
  • Unc5D is thus a newly identified transcriptional target of proapoptotic p53 and may also act upstream of p53 to induce p53dependent apoptosis by phosphorylation at ser15. (PMID:24691657)
  • The authors identified a locus on chromosome 8, containing UNC5D, and demonstrated evidence of its genome-wide significance with mental composite scores. Within this locus, the joint effects of two independent single nucleotide polymorphisms had a p-value of 4.38 x 10(-9) for mental composite scores. (PMID:28754176)
  • these results suggested that UNC5D as a novel putative metastatic suppressor gene that is commonly down-regulated by hypermethylation in PCa. (PMID:30632669)
  • Hypermethylated promoters of genes UNC5D and KCNA1 as potential novel diagnostic biomarkers in colorectal cancer. (PMID:33078631)
  • The expression of UNC5D is abnormal in the early stage of colorectal tumors associated with its proliferation and migration. (PMID:38235871)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriounc5dbENSDARG00000061541
danio_reriounc5daENSDARG00000092722
mus_musculusUnc5dENSMUSG00000063626
rattus_norvegicusUnc5dENSRNOG00000011858
drosophila_melanogasterunc-5FBGN0034013
caenorhabditis_elegansWBGENE00006745

Paralogs (4): UNC5B (ENSG00000107731), UNC5A (ENSG00000113763), UNC5CL (ENSG00000124602), UNC5C (ENSG00000182168)

Protein

Protein identifiers

Netrin receptor UNC5DQ6UXZ4 (reviewed: Q6UXZ4)

Alternative names: Protein unc-5 homolog 4, Protein unc-5 homolog D

All UniProt accessions (5): Q6UXZ4, C9J1I0, C9J2B6, E9PDS8, H7BXJ2

UniProt curated annotations — full annotation on UniProt →

Function. Receptor for the netrin NTN4 that promotes neuronal cell survival. Plays a role in cell-cell adhesion and cell guidance. Receptor for netrin involved in cell migration. Plays a role in axon guidance by mediating axon repulsion of neuronal growth cones in the developing nervous system upon ligand binding. May play a role in apoptosis in response to DNA damage. It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand. Mediates cell-cell adhesion via its interaction with FLRT3 on an adjacent cell.

Subunit / interactions. Interacts (via extracellular domain) with FLRT2 (via extracellular domain); the interaction is direct. Interacts (via extracellular domain) with FLRT3 (via extracellular domain); the interaction is direct. Identified in a complex with FLRT3 and ADGRL3; does not interact with ADGRL3 by itself.

Subcellular location. Cell membrane.

Post-translational modifications. Proteolytically cleaved by caspases during apoptosis. The cleavage does not take place when the receptor is associated with netrin ligand. Its cleavage by caspases is required to induce apoptosis.

Induction. Up-regulated by p53/TP53 in response to DNA damage.

Similarity. Belongs to the unc-5 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q6UXZ4-11yes
Q6UXZ4-22

RefSeq proteins (3): NP_001309747, NP_001397847, NP_543148* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000488Death_domDomain
IPR000884TSP1_rptRepeat
IPR000906ZU5_domDomain
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR011029DEATH-like_dom_sfHomologous_superfamily
IPR013098Ig_I-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR033772UPADomain
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR036383TSP1_rpt_sfHomologous_superfamily
IPR037936UNC5A-DFamily
IPR042058UNC5D_DeathDomain
IPR057755UNC5A-D-like_NDomain

Pfam: PF00090, PF00531, PF00791, PF07679, PF17217, PF25609

UniProt features (28 total): disulfide bond 9, domain 6, glycosylation site 4, topological domain 2, signal peptide 1, chain 1, region of interest 1, site 1, splice variant 1, sequence variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6UXZ4-F175.010.46

Functional residue map

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

Catalytic / active sites (1): 416–417 (cleavage; by caspase-3)

Disulfide bonds (9): 75–136, 87–134, 180–231, 264–301, 268–305, 279–291, 320–354, 324–359, 332–344

Glycosylation sites (4): 117, 228, 353, 376

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-418886Netrin mediated repulsion signals

MSigDB gene sets: 148 (showing top): GOCC_CELL_SURFACE, GOBP_NEUROGENESIS, CACCAGC_MIR138, ATGTTAA_MIR302C, GOBP_CELL_CELL_ADHESION, MODULE_171, MODULE_301, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION, GOBP_REGULATION_OF_NEURON_MIGRATION, GOBP_NEURON_MIGRATION, chr8p12, GOBP_CELL_PROJECTION_ORGANIZATION, VECCHI_GASTRIC_CANCER_EARLY_DN, ATGTCAC_MIR489, MODULE_188

GO Biological Process (7): apoptotic process (GO:0006915), axon guidance (GO:0007411), pyramidal neuron differentiation (GO:0021859), obsolete cell-cell adhesion via plasma-membrane adhesion molecules (GO:0098742), regulation of neuron migration (GO:2001222), signal transduction (GO:0007165), netrin-activated signaling pathway (GO:0038007)

GO Molecular Function (2): netrin receptor activity (GO:0005042), protein binding (GO:0005515)

GO Cellular Component (3): plasma membrane (GO:0005886), cell surface (GO:0009986), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Netrin-1 signaling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
axonogenesis1
neuron projection guidance1
central nervous system neuron differentiation1
neuron migration1
regulation of cell migration1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cell surface receptor signaling pathway1
transmembrane signaling receptor activity1
netrin-activated signaling pathway1
binding1
membrane1
cell periphery1

Protein interactions and networks

STRING

1300 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UNC5DNTN1O95631860
UNC5DFLRT2O43155827
UNC5DFLRT3Q9NZU0781
UNC5DDCCP43146675
UNC5DNEO1Q92859673
UNC5DADGRL3Q9HAR2597
UNC5DNTN4Q9HB63545
UNC5DNTN3O00634540
UNC5DNTNG2Q96CW9513
UNC5DNTNG1Q9Y2I2504
UNC5DSEMA3AQ14563499
UNC5DDSCAMO60469498
UNC5DBCL11BQ9C0K0489
UNC5DFLRT1Q9NZU1471
UNC5DCUX2O14529471

IntAct

5 interactions, top by confidence:

ABTypeScore
MPIG6BUNC5Dpsi-mi:“MI:0915”(physical association)0.400
SIGLEC15UNC5Dpsi-mi:“MI:0915”(physical association)0.400
TYRO3UNC5Dpsi-mi:“MI:0915”(physical association)0.400
Mpsi-mi:“MI:0914”(association)0.350

BioGRID (7): UNC5D (Affinity Capture-MS), UNC5D (Affinity Capture-MS), FLRT2 (Reconstituted Complex), UNC5D (Reconstituted Complex), UNC5D (Affinity Capture-MS), UNC5D (Protein-peptide), UNC5D (Affinity Capture-RNA)

ESM2 similar proteins: A0A0G2JEB6, A0JM56, B0DOB4, B0FXQ5, B1ANS9, B4F7L9, B4GQJ7, B5DHW4, B7FF06, B7FF07, B7FF08, B7FF09, B7FF12, C5IAW9, F1LW30, F1P4W9, O08747, O95185, P0DM40, Q008S8, Q18264, Q32NR9, Q3V0B4, Q402B2, Q4G0P3, Q5R4M2, Q5T0N1, Q5XI14, Q6AXU1, Q6DCF6, Q6NRS1, Q6P2C0, Q6P5D8, Q6UXZ4, Q6ZTR5, Q6ZU64, Q761X5, Q7T2Z5, Q80W93, Q86YR7

Diamond homologs: A0A0G2K2P5, A0A8P0N4K0, C5IAW9, F1LW30, O08721, O08722, O08747, O62683, O95049, O95185, O97758, P39447, P57105, Q07157, Q0P5E6, Q13424, Q28626, Q32LE7, Q3T0C9, Q5EBL8, Q5ZIK2, Q61234, Q6NXB2, Q6QA76, Q6R653, Q6UXZ4, Q6ZN44, Q761X5, Q7KRY7, Q7T2Z5, Q80VW5, Q86UL8, Q8IV45, Q8IZJ1, Q8JGT4, Q8K1S2, Q8K1S3, Q8K1S4, Q95168, Q9CZG9

SIGNOR signaling

1 interactions.

AEffectBMechanism
UNC5D“down-regulates activity”DCCbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance84
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

6278 predictions. Top by Δscore:

VariantEffectΔscore
8:35294717:A:AGacceptor_gain1.0000
8:35549286:TCACA:Tacceptor_loss1.0000
8:35549287:CACAG:Cacceptor_loss1.0000
8:35549289:CAGG:Cacceptor_loss1.0000
8:35549290:A:ATacceptor_loss1.0000
8:35549291:G:Tacceptor_loss1.0000
8:35549506:CTCAG:Cdonor_loss1.0000
8:35549507:TCAGG:Tdonor_loss1.0000
8:35549508:CAG:Cdonor_loss1.0000
8:35549509:AG:Adonor_loss1.0000
8:35549510:GGTAG:Gdonor_loss1.0000
8:35549511:GT:Gdonor_loss1.0000
8:35549512:T:Adonor_loss1.0000
8:35568093:A:AGacceptor_gain1.0000
8:35568093:ATCAG:Aacceptor_gain1.0000
8:35568094:TCA:Tacceptor_loss1.0000
8:35568095:CA:Cacceptor_loss1.0000
8:35568096:A:AGacceptor_gain1.0000
8:35568096:AGGTT:Aacceptor_loss1.0000
8:35568097:G:GTacceptor_gain1.0000
8:35568097:GGT:Gacceptor_gain1.0000
8:35568097:GGTTT:Gacceptor_gain1.0000
8:35568219:G:GTdonor_gain1.0000
8:35568237:AGCCT:Adonor_gain1.0000
8:35568238:GCCT:Gdonor_gain1.0000
8:35568238:GCCTG:Gdonor_gain1.0000
8:35568239:CCT:Cdonor_gain1.0000
8:35568240:CT:Cdonor_gain1.0000
8:35568240:CTGTA:Cdonor_loss1.0000
8:35568241:TGT:Tdonor_loss1.0000

AlphaMissense

6287 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:35549348:C:TP54S1.000
8:35549349:C:AP54H1.000
8:35549354:T:CF56L1.000
8:35549355:T:CF56S1.000
8:35549355:T:GF56C1.000
8:35549356:C:AF56L1.000
8:35549356:C:GF56L1.000
8:35549366:C:TP60S1.000
8:35549367:C:AP60Q1.000
8:35549367:C:GP60R1.000
8:35549382:T:AI65N1.000
8:35549387:A:GK67E1.000
8:35549389:G:CK67N1.000
8:35549389:G:TK67N1.000
8:35549406:T:CL73P1.000
8:35549411:T:AC75S1.000
8:35549411:T:CC75R1.000
8:35549412:G:AC75Y1.000
8:35549412:G:CC75S1.000
8:35549412:G:TC75F1.000
8:35549413:C:GC75W1.000
8:35549436:T:AI83K1.000
8:35549436:T:CI83T1.000
8:35549436:T:GI83R1.000
8:35549441:T:CF85L1.000
8:35549442:T:CF85S1.000
8:35549442:T:GF85C1.000
8:35549443:C:AF85L1.000
8:35549443:C:GF85L1.000
8:35549444:A:GK86E1.000

dbSNP variants (sampled 300 via entrez): RS1000000845 (8:35581718 C>T), RS1000001133 (8:35278024 A>T), RS1000012738 (8:35599478 T>C,G), RS1000020013 (8:35764622 C>T), RS1000023547 (8:35404300 G>A), RS1000026505 (8:35623807 G>A), RS1000036294 (8:35760666 G>A), RS1000048191 (8:35242278 G>A), RS1000059999 (8:35325586 G>T), RS1000062933 (8:35484687 T>C), RS1000067329 (8:35634784 G>C,T), RS1000069024 (8:35365664 G>A,T), RS1000075821 (8:35666666 G>A), RS1000081440 (8:35538632 A>G), RS1000083598 (8:35641439 G>A)

Disease associations

OMIM: gene MIM:616466 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

14 associations (top):

StudyTraitp-value
GCST002783_231Body mass index3.000000e-07
GCST002783_411Body mass index5.000000e-06
GCST002932_3Manganese levels5.000000e-06
GCST003838_15Morning vs. evening chronotype2.000000e-08
GCST004769_1Mental development (prenatal lead exposure interaction)4.000000e-06
GCST006168_5Pulse pressure x alcohol consumption interaction (2df test)3.000000e-09
GCST006585_2577Blood protein levels1.000000e-08
GCST006585_2682Blood protein levels2.000000e-06
GCST007576_216Chronotype3.000000e-08
GCST008163_431Height3.000000e-06
GCST008398_11Glycated hemoglobin levels1.000000e-06
GCST009897_5Reading disability2.000000e-06
GCST010242_244HDL cholesterol levels1.000000e-08
GCST012216_6Vegetable consumption3.000000e-08

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008230mental development measurement
EFO:0004329alcohol drinking
EFO:0005763pulse pressure measurement
EFO:0008328chronotype measurement
EFO:0004541HbA1c measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0008111diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, increases expression5
trichostatin Aaffects cotreatment, decreases expression3
Resveratrolaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
propionaldehydeincreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sincreases methylation1
Sunitinibincreases expression1
Arsenic Trioxidedecreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Vehicle Emissionsincreases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Copperaffects cotreatment, decreases expression1
Diethylhexyl Phthalatedecreases expression1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, decreases expression1
Lipopolysaccharidesaffects response to substance, increases expression, affects cotreatment1
Ozoneincreases oxidation, increases abundance, affects cotreatment1
Plant Extractsdecreases expression, affects cotreatment1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Tretinoindecreases expression1
Triclosanincreases expression1
1-Methyl-4-phenylpyridiniumdecreases expression1
Aflatoxin B1increases methylation1

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): dyslexia