NTN3

netrin 3, the group of Netrins

Basic information

Region (hg38): 16:2471296-2474145

Previous symbols: [ "NTN2L" ]

Links

ENSG00000162068 ∙ NCBI:4917 ∙ OMIM:602349 ∙ HGNC:8030 ∙ Uniprot:O00634 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NTN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTN3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			42	1		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	1	0

Variants in NTN3

This is a list of pathogenic ClinVar variants found in the NTN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-2471783-G-A		not specified	Uncertain significance (Jan 04, 2024)
16-2471805-G-C		not specified	Uncertain significance (May 20, 2024)
16-2471807-G-A		not specified	Uncertain significance (Aug 17, 2021)
16-2471813-C-G		not specified	Uncertain significance (Dec 14, 2023)
16-2471839-C-G		not specified	Uncertain significance (Dec 01, 2022)
16-2471906-G-A		not specified	Uncertain significance (Sep 27, 2022)
16-2471922-G-C		not specified	Uncertain significance (Feb 02, 2024)
16-2471949-C-T		not specified	Uncertain significance (Jan 10, 2023)
16-2471958-G-A		not specified	Uncertain significance (Mar 22, 2022)
16-2471961-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-2471991-C-A		not specified	Uncertain significance (Dec 16, 2022)
16-2472053-G-T		not specified	Uncertain significance (Jan 29, 2024)
16-2472119-C-T		not specified	Uncertain significance (May 18, 2023)
16-2472120-A-G		not specified	Uncertain significance (Jan 17, 2024)
16-2472125-C-G		not specified	Uncertain significance (Mar 28, 2022)
16-2472213-C-T		not specified	Uncertain significance (Dec 20, 2021)
16-2472246-T-C		not specified	Uncertain significance (Sep 14, 2022)
16-2472326-C-T		not specified	Uncertain significance (Feb 17, 2024)
16-2472363-G-A			Likely benign (Mar 01, 2023)
16-2472404-G-A		not specified	Uncertain significance (Sep 13, 2023)
16-2472462-G-A		not specified	Uncertain significance (Feb 22, 2023)
16-2472464-T-A		not specified	Uncertain significance (Jan 27, 2022)
16-2472570-C-A		not specified	Uncertain significance (Feb 21, 2024)
16-2472581-G-A		not specified	Uncertain significance (Jan 11, 2023)
16-2472608-C-T		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTN3	protein_coding	protein_coding	ENST00000293973	6	2647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.23e-7	0.554	125172	1	481	125654	0.00192

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.283	293	307	0.955	0.0000206	3622
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00319	0.00222
Ashkenazi Jewish	0.000103	0.0000993
East Asian	0.000167	0.000163
Finnish	0.0000477	0.0000462
European (Non-Finnish)	0.0105	0.00379
Middle Eastern	0.000167	0.000163
South Asian	0.000198	0.000196
Other	0.00348	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons. {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;CDO in myogenesis;Myogenesis (Consensus)

Recessive Scores

• pRec: 0.104

Haploinsufficiency Scores

• pHI: 0.478
• hipred: N
• hipred_score: 0.451
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntn3

Gene ontology

• Biological process: axon guidance
• Cellular component: cellular_component;extracellular region;Golgi apparatus
• Molecular function: molecular_function;signaling receptor binding;protein binding