SLIT3

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

Basic information

Region (hg38): 5:168661740-169301139

Previous symbols: [ "SLIL2" ]

Links

ENSG00000184347 ∙ NCBI:6586 ∙ OMIM:603745 ∙ HGNC:11087 ∙ Uniprot:O75094 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital diaphragmatic hernia (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLIT3 gene.

• not_specified (228 variants)
• not_provided (46 variants)
• SLIT3-related_disorder (18 variants)
• SLIT3-related_anomalies_of_the_kidney_and_urinary_tract (5 variants)
• Familial_congenital_diaphragmatic_hernia (1 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. These statistics are base on transcript: NM_000003062.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	32	3	39
missense		1	238	11	3	253
nonsense			1			1
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			5			5
Total	0	1	249	43	6

Highest pathogenic variant AF is 0.000010260802

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
		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

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

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