NTN5

protein-coding

netrin 5, the group of Netrins

Gene summary

Predicted to be an extracellular matrix structural constituent. Predicted to be involved in neurogenesis and substrate adhesion-dependent cell spreading. Predicted to be located in extracellular region. Predicted to be active in basement membrane and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_145807.4

Inheritance

—

ClinVar variants

U:118B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr19:48,661,407-48,673,081

External References & Databases

Ensembl (ENSG00000142233)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 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 NTN5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 121

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145807.4. 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				1 clinvar	1 clinvar	2
missense			118 clinvar	5 clinvar		123
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	118	6	1	125

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145807.4	RefSeq	NP_665806.1	6	MANE Select
ENST00000270235.11	Ensembl	ENSP00000270235.4	6	MANE Select
ENST00000596844.5	Ensembl	ENSP00000469490.1	4	Standard
ENST00000954299.1	Ensembl	ENSP00000624358.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

neurogenesis

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000270235
Coding exons: 6
Length: 11675
Individuals with no LoFs: 125609
Homozygous LoFs: 0
Heterozygous LoFs: 137
Defined: 125746
p: 0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.11	202	252	0.803	0.0000163	3009
Missense (PolyPhen)		58	74.481	0.77872		954
Synonymous	0.695	98	107	0.915	0.00000691	1069
Loss of Function	-0.825	20	16.4	1.22	8.98e-7	181

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00075	0.00075	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000058	0.000054	rare
Finnish	0.0027	0.0027	notable
European (Non-Finnish)	0.00036	0.00034	rare
South Asian	0.00031	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in neurogenesis. Prevents motor neuron cell body migration out of the neural tube. {ECO:0000250|UniProtKB:Q3UQ22}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.393

Gene Damage Prediction

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