SLIT3

slit guidance ligand 3, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:168661732-169301139

Previous symbols: [ "SLIL2" ]

Links

ENSG00000184347 ∙ NCBI:6586 ∙ OMIM:603745 ∙ HGNC:11087 ∙ Uniprot:O75094 ∙ 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 SLIT3 gene.

• Inborn genetic diseases (75 variants)
• not provided (45 variants)
• SLIT3-related anomalies of the kidney and urinary tract (5 variants)
• SLIT3-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLIT3 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				23	5	28
missense			80	5	5	90
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			2		4	6
Total	0	0	83	28	14

Variants in SLIT3

This is a list of pathogenic ClinVar variants found in the SLIT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-168666436-AGGCAGGCG-A		SLIT3-related disorder	Uncertain significance (Sep 08, 2022)
5-168666465-C-T		not specified	Uncertain significance (Aug 02, 2022)
5-168666468-G-A		not specified	Uncertain significance (Aug 26, 2022)
5-168666474-C-T		not specified	Uncertain significance (Jun 21, 2023)
5-168666520-C-T		SLIT3-related disorder	Likely benign (Jan 01, 2024)
5-168666545-C-T		not specified	Uncertain significance (Oct 25, 2022)
5-168666554-C-T		not specified	Uncertain significance (Dec 07, 2021)
5-168666571-C-A		SLIT3-related disorder	Uncertain significance (Nov 04, 2022)
5-168666590-C-T		not specified	Likely benign (Oct 05, 2023)
5-168666647-C-T			Benign (Jul 07, 2018)
5-168666648-G-A		not specified	Uncertain significance (Oct 14, 2023)
5-168666665-A-C		not specified	Uncertain significance (Jul 16, 2021)
5-168666683-G-A		not specified	Uncertain significance (Feb 16, 2023)
5-168669798-C-T			Uncertain significance (Aug 01, 2023)
5-168669810-C-T		not specified	Uncertain significance (Oct 04, 2022)
5-168669830-G-A		not specified	Uncertain significance (Mar 06, 2023)
5-168669872-T-C		not specified	Uncertain significance (Mar 14, 2023)
5-168669923-C-T		not specified	Uncertain significance (Feb 28, 2024)
5-168669954-A-G			Uncertain significance (Aug 01, 2023)
5-168669965-G-T		not specified	Uncertain significance (Oct 25, 2022)
5-168671228-T-C		not specified	Uncertain significance (Nov 03, 2023)
5-168671230-A-G			Benign (Feb 12, 2021)
5-168671245-G-A			Benign/Likely benign (Jan 01, 2024)
5-168671272-C-T		SLIT3-related disorder	Likely benign (Apr 20, 2022)
5-168671281-C-A		SLIT3-related disorder • not specified	Uncertain significance (Sep 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLIT3	protein_coding	protein_coding	ENST00000519560	36	639389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.752	0.248	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	742	907	0.818	0.0000561	9937
Missense in Polyphen		259	372.31	0.69566		4109
Synonymous	-0.180	398	393	1.01	0.0000265	2945
Loss of Function	6.67	18	83.9	0.215	0.00000480	891

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.000490	0.000490
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as molecular guidance cue in cellular migration, and function may be mediated by interaction with roundabout homolog receptors.
• Pathway: Axon guidance - Homo sapiens (human);Spinal Cord Injury;Developmental Biology;Regulation of commissural axon pathfinding by SLIT and ROBO;Netrin-1 signaling;Signaling by ROBO receptors;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.150
• rvis_EVS: -2.2
• rvis_percentile_EVS: 1.37

Haploinsufficiency Scores

• pHI: 0.828
• hipred: Y
• hipred_score: 0.605
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.401

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slit3
• Phenotype: muscle phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland 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); digestive/alimentary phenotype; renal/urinary system phenotype; skeleton phenotype; liver/biliary system phenotype; respiratory system phenotype; 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); 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)

Gene ontology

• Biological process: aortic valve morphogenesis;atrioventricular valve morphogenesis;axon guidance;negative regulation of cell population proliferation;negative regulation of gene expression;chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration;negative regulation of cell growth;cellular response to hormone stimulus;Roundabout signaling pathway;axon extension involved in axon guidance;negative chemotaxis;response to cortisol;ventricular septum morphogenesis;apoptotic process involved in luteolysis;negative regulation of chemokine-mediated signaling pathway
• Cellular component: extracellular space;mitochondrion
• Molecular function: calcium ion binding;Roundabout binding