UNC5B

unc-5 netrin receptor B, the group of Ig-like cell adhesion molecule family|I-set domain containing

Basic information

Region (hg38): 10:71212570-71302864

Links

ENSG00000107731 ∙ NCBI:219699 ∙ OMIM:607870 ∙ HGNC:12568 ∙ Uniprot:Q8IZJ1 ∙ 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 UNC5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UNC5B 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				3		3
missense			111	6		117
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	112	9	1

Variants in UNC5B

This is a list of pathogenic ClinVar variants found in the UNC5B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-71213008-G-C		not specified	Uncertain significance (Mar 06, 2023)
10-71213040-T-A		not specified	Uncertain significance (Dec 13, 2021)
10-71213056-G-C		not specified	Uncertain significance (Apr 19, 2024)
10-71279871-G-C		not specified	Uncertain significance (Oct 11, 2024)
10-71279941-T-A		not specified	Uncertain significance (Jul 12, 2022)
10-71279943-C-G		not specified	Uncertain significance (May 30, 2024)
10-71279973-T-C		not specified	Uncertain significance (Apr 26, 2023)
10-71279993-G-T		not specified	Likely benign (Aug 05, 2024)
10-71280008-C-T			Likely benign (Aug 01, 2023)
10-71280022-A-G		not specified	Uncertain significance (Nov 10, 2022)
10-71280031-T-C		not specified	Uncertain significance (Jul 25, 2023)
10-71284723-T-G		not specified	Uncertain significance (Aug 02, 2022)
10-71284731-C-T		not specified	Uncertain significance (Feb 09, 2023)
10-71284732-G-A		not specified	Uncertain significance (Mar 31, 2023)
10-71284742-G-T		not specified	Uncertain significance (Dec 26, 2023)
10-71284748-G-T		not specified	Uncertain significance (Feb 10, 2022)
10-71284756-G-A		not specified	Uncertain significance (Jun 27, 2022)
10-71284803-T-G		not specified	Uncertain significance (Jan 26, 2023)
10-71284839-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-71284851-G-A		not specified	Uncertain significance (Mar 01, 2023)
10-71285331-C-T		not specified	Uncertain significance (Jul 02, 2024)
10-71285401-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-71285401-G-T		not specified	Uncertain significance (Jan 25, 2023)
10-71286694-A-G			Likely benign (Apr 01, 2023)
10-71286698-C-G		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UNC5B	protein_coding	protein_coding	ENST00000335350	17	90295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.69e-7	1.00	123616	59	2073	125748	0.00851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0523	602	606	0.994	0.0000402	6058
Missense in Polyphen		201	223.47	0.89945		2257
Synonymous	-0.831	279	262	1.07	0.0000183	1942
Loss of Function	3.58	19	44.9	0.423	0.00000220	481

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0539	0.0532
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.00926	0.00907
Finnish	0.00248	0.00236
European (Non-Finnish)	0.00315	0.00310
Middle Eastern	0.00926	0.00907
South Asian	0.00281	0.00275
Other	0.00661	0.00637

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for netrin required for axon guidance. Mediates axon repulsion of neuronal growth cones in the developing nervous system upon ligand binding. Axon repulsion in growth cones may be caused by its association with DCC that may trigger signaling for repulsion (By similarity). Functions as netrin receptor that negatively regulates vascular branching during angiogenesis. Mediates retraction of tip cell filopodia on endothelial growth cones in response to netrin (By similarity). It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand (PubMed:12598906). Mediates apoptosis by activating DAPK1. In the absence of NTN1, activates DAPK1 by reducing its autoinhibitory phosphorylation at Ser-308 thereby increasing its catalytic activity (By similarity). {ECO:0000250|UniProtKB:O08722, ECO:0000250|UniProtKB:Q8K1S3, ECO:0000269|PubMed:12598906}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Caspase activation via extrinsic apoptotic signalling pathway;Apoptosis;Programmed Cell Death;Netrin mediated repulsion signals;Ligand-independent caspase activation via DCC;Netrin-1 signaling;Axon guidance;Netrin-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.543
• rvis_EVS: -1.63
• rvis_percentile_EVS: 2.88

Haploinsufficiency Scores

• pHI: 0.950
• hipred: Y
• hipred_score: 0.637
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.439

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Unc5b
• Phenotype: cellular phenotype; embryo 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); 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: unc5b
• Affected structure: parachordal vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: angiogenesis;apoptotic process;positive regulation of phosphatidylinositol 3-kinase signaling;anterior/posterior axon guidance;netrin-activated signaling pathway;negative regulation of neuron apoptotic process;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
• Cellular component: plasma membrane;integral component of membrane;membrane raft
• Molecular function: netrin receptor activity;protein binding