NTN5

netrin 5, the group of Netrins

Basic information

Region (hg38): 19:48661407-48673081

Links

ENSG00000142233 ∙ NCBI:126147 ∙ ∙ HGNC:25208 ∙ Uniprot:Q8WTR8 ∙ 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 NTN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTN5 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				1	2	3
missense			78	4		82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					9	9
Total	0	0	78	5	11

Variants in NTN5

This is a list of pathogenic ClinVar variants found in the NTN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48661483-T-C			Benign (May 13, 2021)
19-48661706-G-T		not specified	Uncertain significance (Oct 09, 2024)
19-48661720-C-G		not specified	Uncertain significance (Feb 27, 2025)
19-48661726-C-T		not specified	Uncertain significance (Jan 29, 2025)
19-48661729-C-T		not specified	Uncertain significance (Jul 20, 2021)
19-48661731-G-A			Likely benign (Mar 01, 2023)
19-48661742-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-48661765-C-T		not specified	Uncertain significance (Dec 08, 2023)
19-48661820-G-A		not specified	Uncertain significance (Aug 21, 2024)
19-48661835-C-T		not specified	Uncertain significance (Aug 04, 2024)
19-48661876-T-C		not specified	Likely benign (Nov 15, 2021)
19-48661879-A-C		not specified	Uncertain significance (Feb 16, 2023)
19-48661882-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-48661900-A-C			Likely benign (Mar 01, 2023)
19-48661913-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-48661936-C-T		not specified	Uncertain significance (Mar 14, 2025)
19-48661939-C-A		not specified	Uncertain significance (Mar 19, 2024)
19-48661939-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-48661943-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-48661954-C-A		not specified	Uncertain significance (Dec 30, 2023)
19-48661967-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-48661981-A-C		not specified	Uncertain significance (Dec 24, 2024)
19-48661985-C-A		not specified	Uncertain significance (Dec 27, 2023)
19-48661999-G-A		not specified	Uncertain significance (Mar 04, 2025)
19-48662015-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTN5	protein_coding	protein_coding	ENST00000270235	6	11675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.79e-15	0.00310	125609	0	137	125746	0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	202	252	0.803	0.0000163	3009
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000885	0.000877
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000576	0.0000544
Finnish	0.00273	0.00273
European (Non-Finnish)	0.000362	0.000343
Middle Eastern	0.0000576	0.0000544
South Asian	0.000308	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.188
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.393

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntn5
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: neurogenesis
• Cellular component: extracellular region