UNC5A

gene
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Also known as KIAA1976UNC5H1

Summary

UNC5A (unc-5 netrin receptor A, HGNC:12567) is a protein-coding gene on chromosome 5q35.2, encoding Netrin receptor UNC5A (Q6ZN44). Receptor for netrin required for axon guidance.

UNC5A belongs to a family of netrin-1 (MIM 601614) receptors thought to mediate the chemorepulsive effect of netrin-1 on specific axons. For more information on UNC5 proteins, see UNC5C (MIM 603610).

Source: NCBI Gene 90249 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 100 total
  • MANE Select transcript: NM_133369

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12567
Approved symbolUNC5A
Nameunc-5 netrin receptor A
Location5q35.2
Locus typegene with protein product
StatusApproved
AliasesKIAA1976, UNC5H1
Ensembl geneENSG00000113763
Ensembl biotypeprotein_coding
OMIM607869
Entrez90249

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 nonsense_mediated_decay

ENST00000329542, ENST00000509580, ENST00000513890, ENST00000927830, ENST00000970734

RefSeq mRNA: 1 — MANE Select: NM_133369 NM_133369

CCDS: CCDS34299

Canonical transcript exons

ENST00000329542 — 15 exons

ExonStartEnd
ENSE00001158964176879310176879488
ENSE00001158973176878475176878639
ENSE00001158980176878244176878393
ENSE00001158987176877894176878127
ENSE00001158992176877535176877703
ENSE00001159001176877192176877279
ENSE00001159009176874264176874566
ENSE00001400922176810559176810820
ENSE00001430991176862624176862845
ENSE00003545204176868561176868664
ENSE00003601466176870370176870534
ENSE00003617779176868784176868964
ENSE00003636035176873968176874156
ENSE00003666765176868130176868273
ENSE00003827647176879721176880898

Expression profiles

Bgee: expression breadth ubiquitous, 145 present calls, max score 97.69.

FANTOM5 (CAGE): breadth broad, TPM avg 2.4667 / max 228.6698, expressed in 395 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
604371.0737276
604380.8284205
604360.2255107
604350.200094
604340.106447
604390.032723

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011597.69gold quality
middle temporal gyrusUBERON:000277195.99gold quality
Brodmann (1909) area 23UBERON:001355495.35gold quality
primary visual cortexUBERON:000243695.07gold quality
right hemisphere of cerebellumUBERON:001489094.15gold quality
right frontal lobeUBERON:000281093.99gold quality
cerebellar hemisphereUBERON:000224593.28gold quality
cerebellar cortexUBERON:000212993.15gold quality
occipital lobeUBERON:000202192.80gold quality
cerebellumUBERON:000203792.36gold quality
frontal cortexUBERON:000187092.30gold quality
prefrontal cortexUBERON:000045192.27gold quality
superior frontal gyrusUBERON:000266191.70gold quality
Brodmann (1909) area 9UBERON:001354091.56gold quality
neocortexUBERON:000195091.31gold quality
dorsolateral prefrontal cortexUBERON:000983491.29gold quality
cerebral cortexUBERON:000095690.11gold quality
postcentral gyrusUBERON:000258190.01gold quality
parietal lobeUBERON:000187289.90gold quality
anterior cingulate cortexUBERON:000983589.55gold quality
ganglionic eminenceUBERON:000402389.33gold quality
entorhinal cortexUBERON:000272888.61gold quality
Ammon’s hornUBERON:000195486.90gold quality
temporal lobeUBERON:000187186.23gold quality
cortical plateUBERON:000534385.76gold quality
forebrainUBERON:000189084.61gold quality
amygdalaUBERON:000187684.45gold quality
brainUBERON:000095584.40gold quality
cerebellar vermisUBERON:000472083.38gold quality
Brodmann (1909) area 46UBERON:000648382.36gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no1.62

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXC1, TP53

miRNA regulators (miRDB)

123 targeting UNC5A, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-8485100.0077.574731
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4692100.0067.322066
HSA-MIR-4262100.0073.263931
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-451499.9967.101870
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-493-5P99.9672.472382
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-449299.8768.253611
HSA-MIR-394199.8670.542735
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-76599.8468.242442
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-44899.7972.372103
HSA-MIR-320A-3P99.7769.732107
HSA-MIR-320B99.7769.732107
HSA-MIR-320C99.7769.732107
HSA-MIR-320D99.7769.732107

Literature-anchored findings (GeneRIF, showing 9)

  • may represent tumor suppressor that inhibit tumor extension outside the region of netrin-1 availability by inducing apoptosis (PMID:12655055)
  • UNC5 orthologues define a new mechanism for both the positive (induction) and negative (suppression) regulation of apoptosis in cancer cells (review) (PMID:15573119)
  • UNC5A is a novel transcriptional target of p53 and plays a role in p53-dependent apoptosis (PMID:20372800)
  • FANCC interferes with UNC5A’s functions in apoptosis and suggest that FANCC may participate in developmental processes through association with the dependence receptor UNC5A. (PMID:24676280)
  • these data suggest an important role for UNC5A, a candidate tumor suppressor, in predicting response to DNA damage induced by chemotherapeutic drug and regulating cell death in bladder cancer (PMID:24737586)
  • The results suggest that netrin-1 promotes glioma cell proliferation by activating NF-kappaB signaling via UNC5A. (PMID:28710382)
  • UNC5A is capable of impeding autophagy and promoting HCV restriction through specific impact on virion infectivity, in a cell death-independent and DAPK-related manner. (PMID:28783179)
  • Such data indicate that cooperation between the UPR and UNC5A depletion as previously observed by ourselves in HCC patients samples may foster liver cancer development and growth. (PMID:29277614)
  • These studies reveal an unexpected role of the axon guidance receptor UNC5A in fine-tuning ERalpha and EGFR signaling and the luminal progenitor status of hormone-sensitive breast cancers. Furthermore, UNC5A knockdown cells provide an ideal model system to investigate metastasis of ERalpha(+) breast cancers (PMID:29720215)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriounc5aENSDARG00000099034
mus_musculusUnc5aENSMUSG00000025876
rattus_norvegicusUnc5aENSRNOG00000059840
drosophila_melanogasterunc-5FBGN0034013
caenorhabditis_elegansWBGENE00006745

Paralogs (4): UNC5B (ENSG00000107731), UNC5CL (ENSG00000124602), UNC5D (ENSG00000156687), UNC5C (ENSG00000182168)

Protein

Protein identifiers

Netrin receptor UNC5AQ6ZN44 (reviewed: Q6ZN44)

Alternative names: Protein unc-5 homolog 1, Protein unc-5 homolog A

All UniProt accessions (3): Q6ZN44, H0Y8R2, H0Y9G2

UniProt curated annotations — full annotation on UniProt →

Function. Receptor for netrin required for axon guidance. Functions in the netrin signaling pathway and promotes neurite outgrowth in response to NTN1. Mediates axon repulsion of neuronal growth cones in the developing nervous system in response to netrin. Axon repulsion in growth cones may be mediated by its association with DCC that may trigger signaling for repulsion. It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand.

Subunit / interactions. Homodimer and homooligomer. Interacts with the cytoplasmic part of DCC. Interacts with MAGED1. Interacts with PRKCABP, possibly mediating some interaction with PKC. Interacts (via extracellular domain) with FLRT2 (via extracellular domain). Interacts (via extracellular domain) with FLRT3 (via extracellular domain).

Subcellular location. Cell membrane. Membrane raft. Cell projection. Neuron projection.

Post-translational modifications. Phosphorylated on cytoplasmic tyrosine residues. Phosphorylated by PKC in vitro. 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. The two extracellular TSRs of UNC5A contain WxxWxxWxxC motifs that can be C-mannosylated on all tryptophans. DPY19L1 preferentially mannosylates the first two tryptophans and DPY19L3 prefers the third. C-mannosylation by DPY19L1 is required for transport of UNC5A from the endoplasmic reticulum to the cell surface.

Domain organisation. The ZU5 domain mediates the interaction with MAGED1, which participates in the induction of apoptosis.

Induction. By p53/TP53.

Miscellaneous. Down-regulated in multiple cancers including colorectal, breast, ovary, uterus, stomach, lung, or kidney cancers.

Similarity. Belongs to the unc-5 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q6ZN44-11yes
Q6ZN44-22
Q6ZN44-33

RefSeq proteins (1): NP_588610* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000488Death_domDomain
IPR000884TSP1_rptRepeat
IPR000906ZU5_domDomain
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
IPR042155Death_UNC5ADomain
IPR057755UNC5A-D-like_NDomain

Pfam: PF00531, PF00791, PF07679, PF17217, PF25609

UniProt features (52 total): strand 20, glycosylation site 6, disulfide bond 6, domain 5, splice variant 3, topological domain 2, turn 2, helix 2, signal peptide 1, chain 1, region of interest 1, site 1, sequence conflict 1, transmembrane region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4V2AX-RAY DIFFRACTION2.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6ZN44-F178.190.51

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): 340–341 (cleavage; by caspase-3)

Disulfide bonds (6): 65–126, 77–124, 170–221, 254–288, 258–293, 266–278

Glycosylation sites (6): 107, 218, 245, 248, 251, 287

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-373752Netrin-1 signaling
R-HSA-418886Netrin mediated repulsion signals
R-HSA-418889Caspase activation via Dependence Receptors in the absence of ligand

MSigDB gene sets: 104 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, PID_NETRIN_PATHWAY, GOBP_NEUROGENESIS, CACCAGC_MIR138, SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP, GOCC_NEURON_PROJECTION, GOBP_CELL_PROJECTION_ORGANIZATION, REACTOME_APOPTOSIS, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, AGCTCCT_MIR28, HILLION_HMGA1B_TARGETS, GOCC_CELL_PROJECTION_MEMBRANE, ATGTACA_MIR493, GOCC_LEADING_EDGE_MEMBRANE, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (5): apoptotic process (GO:0006915), neuron projection development (GO:0031175), anterior/posterior axon guidance (GO:0033564), netrin-activated signaling pathway (GO:0038007), signal transduction (GO:0007165)

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

GO Cellular Component (7): plasma membrane (GO:0005886), neuron projection membrane (GO:0032589), neuronal cell body membrane (GO:0032809), membrane raft (GO:0045121), membrane (GO:0016020), cell projection (GO:0042995), neuron projection (GO:0043005)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Axon guidance1
Netrin-1 signaling1
Caspase activation via extrinsic apoptotic signalling pathway1

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
neuron development1
plasma membrane bounded cell projection organization1
axon guidance1
cell surface receptor signaling pathway1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
transmembrane signaling receptor activity1
netrin-activated signaling pathway1
binding1
membrane1
cell periphery1
cell projection membrane1
leading edge membrane1
neuron projection1
neuronal cell body1
cell body membrane1
membrane microdomain1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

1488 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UNC5ANTN1O95631998
UNC5AFLRT1Q9NZU1854
UNC5ANEO1Q92859808
UNC5ANTN4Q9HB63702
UNC5AFLRT3Q9NZU0643
UNC5AALOX12P18054639
UNC5ASEMA3AQ14563638
UNC5ADSCAMO60469635
UNC5ADCCP43146620
UNC5ANTN3O00634619
UNC5AMAGED1Q9Y5V3602
UNC5ASEMA3FQ13275596
UNC5AUIMC1Q96RL1596
UNC5ANTN5Q8WTR8561
UNC5AEFNB2P52799560

IntAct

6 interactions, top by confidence:

ABTypeScore
FGFR4UNC5Apsi-mi:“MI:0915”(physical association)0.400
UNC5AMPIG6Bpsi-mi:“MI:0915”(physical association)0.400
LRRN1UNC5Apsi-mi:“MI:0915”(physical association)0.400
LRRTM2UNC5Apsi-mi:“MI:0915”(physical association)0.400
Mpsi-mi:“MI:0914”(association)0.350

BioGRID (9): UNC5A (Affinity Capture-Western), MAGED1 (Two-hybrid), UNC5A (Two-hybrid), FANCC (Affinity Capture-Western), UNC5A (Affinity Capture-Western), NTN1 (Reconstituted Complex), MAGED1 (Reconstituted Complex), MAGED1 (Affinity Capture-Western), UNC5A (Affinity Capture-RNA)

ESM2 similar proteins: A0A8M9PFP2, A1X150, A2A863, A4IH88, B0S5G3, B2RXS4, F1LW30, F1R520, G5ED46, L7VG99, O08721, O08722, O08747, O60486, O73878, O94985, O95185, P10493, P14543, P16144, P35590, P54761, P55292, Q06806, Q0VCN6, Q14393, Q5FWR8, Q5R9Q9, Q61592, Q63772, Q64632, Q6DDG2, Q6Q0N0, Q6UXZ4, Q6ZN44, Q761X5, Q7T2Z5, Q8IZJ1, Q8K1S2, Q8K1S3

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

6 interactions.

AEffectBMechanism
UNC5A“down-regulates activity”DCCbinding
UNC5Aup-regulatesChemorepulsion_of_axon
NTN4up-regulatesUNC5Abinding
PRKCA“down-regulates quantity”UNC5Aphosphorylation
UNC5A“up-regulates activity”PICK1binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance88
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3279 predictions. Top by Δscore:

VariantEffectΔscore
5:176862843:GTG:Gdonor_gain1.0000
5:176868270:GCCT:Gdonor_gain1.0000
5:176868272:CT:Cdonor_gain1.0000
5:176868274:G:GGdonor_gain1.0000
5:176868556:TCTA:Tacceptor_loss1.0000
5:176868558:TAGAT:Tacceptor_loss1.0000
5:176868559:A:AGacceptor_gain1.0000
5:176868559:A:ATacceptor_loss1.0000
5:176868560:G:GAacceptor_gain1.0000
5:176868560:G:GTacceptor_loss1.0000
5:176868560:GATTT:Gacceptor_gain1.0000
5:176868665:GT:Gdonor_loss1.0000
5:176868666:T:Adonor_loss1.0000
5:176868782:AGGT:Aacceptor_gain1.0000
5:176868783:GGTG:Gacceptor_gain1.0000
5:176868960:CTACG:Cdonor_loss1.0000
5:176868962:ACGG:Adonor_loss1.0000
5:176868966:T:Adonor_loss1.0000
5:176868992:G:GTdonor_gain1.0000
5:176868993:G:Tdonor_gain1.0000
5:176869607:C:Aacceptor_gain1.0000
5:176869608:G:Aacceptor_gain1.0000
5:176869612:A:AGacceptor_gain1.0000
5:176869612:AGT:Aacceptor_gain1.0000
5:176869613:G:GAacceptor_gain1.0000
5:176869613:GTG:Gacceptor_gain1.0000
5:176870356:T:TAacceptor_gain1.0000
5:176870364:A:AGacceptor_gain1.0000
5:176870365:T:Gacceptor_gain1.0000
5:176870368:A:AGacceptor_gain1.0000

AlphaMissense

5480 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:176862746:T:AC65S1.000
5:176862746:T:CC65R1.000
5:176862747:G:AC65Y1.000
5:176862747:G:CC65S1.000
5:176862748:C:GC65W1.000
5:176862777:T:CF75S1.000
5:176862782:T:AC77S1.000
5:176862782:T:CC77R1.000
5:176862783:G:CC77S1.000
5:176862796:G:CW81C1.000
5:176862796:G:TW81C1.000
5:176868207:T:AC124S1.000
5:176868207:T:CC124R1.000
5:176868208:G:CC124S1.000
5:176868209:C:GC124W1.000
5:176868213:T:AC126S1.000
5:176868213:T:CC126R1.000
5:176868214:G:AC126Y1.000
5:176868214:G:CC126S1.000
5:176868215:C:GC126W1.000
5:176868564:T:CL147S1.000
5:176868576:T:CF151S1.000
5:176868576:T:GF151C1.000
5:176868627:T:CL168P1.000
5:176868632:T:AC170S1.000
5:176868632:T:CC170R1.000
5:176868633:G:AC170Y1.000
5:176868633:G:CC170S1.000
5:176868634:C:GC170W1.000
5:176868647:G:CG175R1.000

dbSNP variants (sampled 300 via entrez): RS1000028597 (5:176852878 G>A), RS1000043108 (5:176822338 T>C), RS1000122169 (5:176816024 C>T), RS1000143 (5:176857900 A>C,G,T), RS1000144 (5:176857712 C>G,T), RS1000145 (5:176857314 T>G), RS1000184745 (5:176875273 C>A,T), RS1000225156 (5:176809882 G>A,C,T), RS1000239024 (5:176846819 G>A), RS1000273992 (5:176839187 A>G,T), RS1000286426 (5:176877031 G>A,C,T), RS1000289483 (5:176820655 G>A,C), RS1000332211 (5:176864188 C>G), RS1000365929 (5:176851801 G>C), RS1000385332 (5:176827142 G>A)

Disease associations

OMIM: gene MIM:607869 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST005956_15Waist-to-hip ratio adjusted for BMI1.000000e-07
GCST005957_13Waist-to-hip ratio adjusted for BMI (age <50)3.000000e-07
GCST005962_42Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)1.000000e-08
GCST012317_10Triglyceride levels x SSRI levels (escitalopram or citalopram) interaction in schizophrenia or bipolar disorder5.000000e-06

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0004530triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation3
Valproic Acidaffects expression, increases expression3
bisphenol Aincreases methylation, increases expression2
Panobinostataffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
methylmercuric chlorideincreases expression1
propionaldehydedecreases expression1
trichostatin Adecreases expression, increases expression1
sodium arsenitedecreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
Grape Seed Proanthocyanidinsincreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Zoledronic Acidincreases expression1
Acetaminophendecreases expression1
Atrazineincreases expression1
Catechinincreases expression, affects cotreatment1
Estradiolincreases expression1
Leadaffects expression1
Methapyrileneincreases methylation1
Phthalic Acidsdecreases methylation1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Tretinoindecreases expression1
Aflatoxin B1decreases methylation1

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.