NTN4

netrin 4, the group of Netrins

Basic information

Region (hg38): 12:95657807-95791189

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.

not_specified (69 variants)
not_provided (8 variants)
Prostate_cancer (1 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. These statistics are base on transcript: NM_000021229.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	2 clinvar	3
missense			64 clinvar	9 clinvar		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	10	2

Loading clinvar variants...

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