UNC5A

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

Basic information

Region (hg38): 5:176810518-176880898

Links

ENSG00000113763 ∙ NCBI:90249 ∙ OMIM:607869 ∙ HGNC:12567 ∙ Uniprot:Q6ZN44 ∙ 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 UNC5A gene.

• Inborn genetic diseases (18 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UNC5A 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in UNC5A

This is a list of pathogenic ClinVar variants found in the UNC5A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-176862663-G-A		not specified	Uncertain significance (Aug 30, 2021)
5-176862716-A-G		not specified	Uncertain significance (Aug 02, 2023)
5-176862719-G-A		not specified	Uncertain significance (Jan 05, 2022)
5-176862729-A-C		not specified	Uncertain significance (Nov 09, 2022)
5-176862755-G-A		not specified	Uncertain significance (May 03, 2023)
5-176862761-G-A		not specified	Uncertain significance (May 18, 2022)
5-176862824-C-T		not specified	Uncertain significance (Feb 09, 2023)
5-176862836-G-A		not specified	Uncertain significance (Jan 05, 2022)
5-176868567-G-A		not specified	Uncertain significance (Jan 08, 2024)
5-176868623-G-C		not specified	Uncertain significance (Feb 06, 2024)
5-176868940-G-A		not specified	Uncertain significance (Dec 13, 2022)
5-176870502-C-T		not specified	Uncertain significance (Nov 07, 2023)
5-176870517-G-C			Uncertain significance (Aug 24, 2021)
5-176874012-G-A		not specified	Uncertain significance (Apr 25, 2022)
5-176874015-G-A		not specified	Uncertain significance (Feb 13, 2024)
5-176874023-C-T		UNC5A-related disorder	Likely benign (Jun 22, 2021)
5-176874045-G-C		not specified	Uncertain significance (Sep 22, 2023)
5-176874132-G-A		not specified	Uncertain significance (Dec 27, 2023)
5-176874404-G-A		not specified	Uncertain significance (Jun 29, 2023)
5-176874429-C-T		not specified	Uncertain significance (Feb 15, 2023)
5-176874455-G-A		not specified	Uncertain significance (Jul 13, 2021)
5-176874462-G-A		not specified	Uncertain significance (Aug 17, 2022)
5-176877221-A-G		not specified	Uncertain significance (Nov 09, 2021)
5-176877543-T-A		not specified	Uncertain significance (Jun 11, 2021)
5-176877575-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UNC5A	protein_coding	protein_coding	ENST00000329542	15	70420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000169	125689	0	6	125695	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.75	354	533	0.665	0.0000345	5448
Missense in Polyphen		117	205.25	0.57004		1975
Synonymous	0.421	224	232	0.965	0.0000157	1765
Loss of Function	5.26	3	38.0	0.0789	0.00000189	406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000308	0.0000308
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for netrin required for axon guidance. Functions in the netrin signaling pathway and promotes neurite outgrowth in response to NTN1. Mediates axon repulsion of neuronal growth cones in the developing nervous system in response to netrin. Axon repulsion in growth cones may be mediated by its association with DCC that may trigger signaling for repulsion. It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand. {ECO:0000250|UniProtKB:O08721}.
• 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: 0.121

Intolerance Scores

• loftool: 0.0725
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.4

Haploinsufficiency Scores

• pHI: 0.505
• hipred: Y
• hipred_score: 0.822
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Unc5a
• 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); cellular phenotype

Gene ontology

• Biological process: apoptotic process;axon guidance;neuron projection development;anterior/posterior axon guidance;netrin-activated signaling pathway
• Cellular component: plasma membrane;integral component of membrane;intrinsic component of plasma membrane;neuron projection membrane;neuronal cell body membrane;membrane raft
• Molecular function: netrin receptor activity