UNC5D

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

Basic information

Region (hg38): 8:35235474-35796550

Links

ENSG00000156687 ∙ NCBI:137970 ∙ OMIM:616466 ∙ HGNC:18634 ∙ Uniprot:Q6UXZ4 ∙ 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 UNC5D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UNC5D 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	1	2
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	2	1

Variants in UNC5D

This is a list of pathogenic ClinVar variants found in the UNC5D region.

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

Position	Type	Phenotype	Significance	ClinVar
8-35235796-G-T			Likely benign (Dec 31, 2019)
8-35235807-C-G		not specified	Likely benign (Feb 13, 2024)
8-35235824-G-A		not specified	Uncertain significance (Jul 05, 2023)
8-35235827-C-T		not specified	Uncertain significance (Oct 03, 2023)
8-35235875-G-T		not specified	Uncertain significance (Dec 01, 2022)
8-35549318-G-A		not specified	Uncertain significance (Jun 29, 2023)
8-35549365-G-T		not specified	Uncertain significance (Jan 04, 2022)
8-35549399-A-G		not specified	Uncertain significance (Jan 04, 2024)
8-35549418-C-T		not specified	Uncertain significance (Sep 29, 2022)
8-35549453-G-A		not specified	Uncertain significance (Oct 06, 2021)
8-35549474-G-A		not specified	Uncertain significance (May 31, 2023)
8-35568107-T-G		not specified	Uncertain significance (Oct 10, 2023)
8-35568110-G-A		not specified	Uncertain significance (Mar 31, 2024)
8-35568111-C-T			Benign (Jan 08, 2018)
8-35568163-G-A		not specified	Uncertain significance (Dec 21, 2023)
8-35595598-C-T		not specified	Uncertain significance (Mar 29, 2023)
8-35683652-T-G		not specified	Uncertain significance (Oct 26, 2022)
8-35683671-T-G		not specified	Uncertain significance (Jun 29, 2023)
8-35683689-C-T		not specified	Uncertain significance (Dec 18, 2023)
8-35686677-C-A		not specified	Uncertain significance (Jun 29, 2023)
8-35722210-G-A		not specified	Uncertain significance (Apr 08, 2023)
8-35722227-G-A		not specified	Uncertain significance (May 04, 2022)
8-35722252-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-35722263-G-A		not specified	Uncertain significance (Nov 21, 2023)
8-35726202-C-T		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UNC5D	protein_coding	protein_coding	ENST00000404895	17	561094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.929	0.0707	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	378	523	0.723	0.0000288	6244
Missense in Polyphen		120	188.81	0.63555		2166
Synonymous	0.266	200	205	0.976	0.0000124	1844
Loss of Function	5.01	8	43.7	0.183	0.00000197	536

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000100	0.0000924
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the netrin NTN4 that promotes neuronal cell survival (By similarity). Plays a role in cell-cell adhesion and cell guidance. Receptor for netrin involved in cell migration. Plays a role in axon guidance by mediating axon repulsion of neuronal growth cones in the developing nervous system upon ligand binding (By similarity). May play a role in apoptosis in response to DNA damage (PubMed:24691657). It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand (PubMed:24519068). Mediates cell-cell adhesion via its interaction with FLRT3 on an adjacent cell (By similarity). {ECO:0000250|UniProtKB:Q8K1S2, ECO:0000305|PubMed:24519068, ECO:0000305|PubMed:24691657}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Netrin mediated repulsion signals;Netrin-1 signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.433
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.27

Haploinsufficiency Scores

• pHI: 0.910
• hipred: Y
• hipred_score: 0.711
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.410

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Unc5d
• Phenotype: cellular 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: apoptotic process;axon guidance;pyramidal neuron differentiation;netrin-activated signaling pathway;cell-cell adhesion via plasma-membrane adhesion molecules;regulation of neuron migration
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: netrin receptor activity