NTN3
protein-codingnetrin 3, the group of Netrins
Gene summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in Golgi apparatus and extracellular region. [provided by Alliance of Genome Resources, Jul 2025]
- NTN2L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.8 kbGenCC 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 NTN3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006181.3. 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 | 0 | |||||
| missense | 127 | 6 | 133 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 128 | 6 | 0 | 134 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006172.1 | 6 | MANE Select | |
| Ensembl | ENSP00000293973.1 | 6 | MANE Select | |
| Ensembl | ENSP00000804926.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Axon guidance - Homo sapiens (human)
- Developmental Biology
- CDO in myogenesis
- Myogenesis
Biological Process
- axon guidance
Molecular Function
- molecular_function
- signaling receptor binding
- protein binding
Cellular Component
- cellular_component
- extracellular region
- Golgi apparatus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000293973
- Coding exons
- 6
- Length
- 2647
- Individuals with no LoFs
- 125172
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 481
- Defined
- 125654
- p
- 0.00192
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.283 | 293 | 307 | 0.955 | 0.0000206 | 3622 |
| Missense (PolyPhen) | 160 | 163.09 | 0.98106 | 1849 | ||
| Synonymous | 0.682 | 121 | 131 | 0.924 | 0.00000870 | 1330 |
| Loss of Function | 0.943 | 12 | 16.1 | 0.746 | 7.73e-7 | 185 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0017 | 0.00074 | notable |
| Latino/Admixed American | 0.0015 | 0.00055 | notable |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.000048 | 0.000046 | rare |
| European (Non-Finnish) | 0.011 | 0.0038 | notable |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.0035 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.104
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- N
- Indispensability score
- 0.218
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |