UNC5D

protein-coding

unc-5 netrin receptor D, the group of Ig-like cell adhesion molecule family|I-set domain containing

Gene summary

Predicted to enable netrin receptor activity. Involved in cell-cell adhesion. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_080872.4

Inheritance

—

ClinVar variants

U:101B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr8:35,235,475-35,796,550

External References & Databases

Ensembl (ENSG00000156687)

Transcript & Mutation Effects

hg38 • Region Span ~561.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UNC5D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 100

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080872.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	1 clinvar	4
missense			99 clinvar	2 clinvar		101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	101	3	1	105

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080872.4	RefSeq	NP_543148.2	17	MANE Select
ENST00000404895.7	Ensembl	ENSP00000385143.2	17	MANE Select
NM_001322818.2	RefSeq	NP_001309747.1	17	Standard
NM_001410918.1	RefSeq	NP_001397847.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Axon guidance - Homo sapiens (human)
Developmental Biology
Netrin mediated repulsion signals
Netrin-1 signaling
Axon guidance

Biological Process

apoptotic process
axon guidance
pyramidal neuron differentiation
netrin-activated signaling pathway
cell-cell adhesion via plasma-membrane adhesion molecules

Molecular Function

netrin receptor activity

Cellular Component

plasma membrane
cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000404895
Coding exons: 17
Length: 561094
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125748
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.25	378	523	0.723	0.0000288	6244
Missense (PolyPhen)		120	188.81	0.63555		2166
Synonymous	0.266	200	205	0.976	0.0000124	1844
Loss of Function	5.01	8	43.7	0.183	0.00000197	536

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00010	0.000092	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000065	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor for the netrin NTN4 that promotes neuronal cell survival (By similarity). 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 (By similarity). May play a role in apoptosis in response to DNA damage (PubMed:24691657). It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand (PubMed:24519068). Mediates cell-cell adhesion via its interaction with FLRT3 on an adjacent cell (By similarity). {ECO:0000250|UniProtKB:Q8K1S2, ECO:0000305|PubMed:24519068, ECO:0000305|PubMed:24691657}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.433
RVIS EVS: -0.69
RVIS percentile EVS: 15.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.410

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium