NTN4

netrin 4, the group of Netrins

Basic information

Region (hg38): 12:95657806-95791189

Links

ENSG00000074527 ∙ NCBI:59277 ∙ OMIM:610401 ∙ HGNC:13658 ∙ Uniprot:Q9HB63 ∙ 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 NTN4 gene.

• Inborn genetic diseases (20 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTN4 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					2	2
missense			19	4	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	19	4	3

Variants in NTN4

This is a list of pathogenic ClinVar variants found in the NTN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-95659101-T-G		not specified	Uncertain significance (Jan 30, 2024)
12-95665822-T-C		not specified	Uncertain significance (Dec 08, 2023)
12-95665936-C-T		not specified	Uncertain significance (Dec 11, 2023)
12-95665945-C-T		not specified	Uncertain significance (Nov 22, 2022)
12-95670122-G-A		not specified	Likely benign (Dec 02, 2021)
12-95670129-C-T		not specified	Uncertain significance (Mar 01, 2023)
12-95670134-C-T		not specified	Uncertain significance (Oct 06, 2022)
12-95682736-G-A		not specified	Uncertain significance (May 24, 2023)
12-95682737-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-95682776-C-A		not specified	Uncertain significance (Mar 22, 2023)
12-95683552-C-A		not specified	Uncertain significance (Dec 06, 2022)
12-95683603-C-T		not specified	Likely benign (Feb 07, 2023)
12-95683710-C-T			Likely benign (Jan 01, 2023)
12-95710458-G-C			Uncertain significance (Jun 01, 2022)
12-95710569-G-A		not specified	Uncertain significance (Dec 08, 2023)
12-95710573-C-T		not specified	Uncertain significance (Feb 12, 2024)
12-95710602-G-T			Benign (May 09, 2018)
12-95713221-C-T		not specified	Uncertain significance (Oct 02, 2023)
12-95713277-G-A		not specified	Uncertain significance (Jan 05, 2022)
12-95713309-G-A			Benign (Jul 11, 2018)
12-95737872-G-T		not specified	Uncertain significance (May 09, 2023)
12-95737903-C-T		not specified	Uncertain significance (Apr 12, 2023)
12-95737907-G-A		Malignant tumor of prostate	Uncertain significance (-)
12-95737928-C-T		not specified	Uncertain significance (Oct 26, 2022)
12-95738038-C-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTN4	protein_coding	protein_coding	ENST00000343702	10	133348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.916	0.0841	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	273	367	0.744	0.0000206	4120
Missense in Polyphen		81	143.33	0.56512		1618
Synonymous	0.779	125	137	0.915	0.00000792	1172
Loss of Function	4.49	6	34.4	0.174	0.00000205	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000116	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000116	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in neural, kidney and vascular development. Promotes neurite elongation from olfactory bulb explants. {ECO:0000269|PubMed:11038171}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Extracellular matrix organization;Netrin-1 signaling;Non-integrin membrane-ECM interactions;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.390
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.88

Haploinsufficiency Scores

• pHI: 0.487
• hipred: Y
• hipred_score: 0.825
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.455

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntn4
• Phenotype: cellular phenotype; immune system 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); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: axon guidance;neuron remodeling;regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling
• Cellular component: basement membrane;plasma membrane
• Molecular function: protein binding;laminin-1 binding