SLIT1

slit guidance ligand 1

Basic information

Region (hg38): 10:96998037-97185959

Previous symbols: [ "SLIL1" ]

Links

ENSG00000187122 ∙ NCBI:6585 ∙ OMIM:603742 ∙ HGNC:11085 ∙ Uniprot:O75093 ∙ 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 SLIT1 gene.

• Inborn genetic diseases (50 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLIT1 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				4	3	7
missense			50			50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	50	4	3

Variants in SLIT1

This is a list of pathogenic ClinVar variants found in the SLIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97001117-C-G		not specified	Uncertain significance (Nov 17, 2022)
10-97001159-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-97001213-G-A		not specified	Uncertain significance (Feb 23, 2023)
10-97001243-A-G		not specified	Uncertain significance (Jan 30, 2024)
10-97001245-G-A		not specified	Uncertain significance (Sep 17, 2021)
10-97001251-C-T		not specified	Uncertain significance (Jun 23, 2023)
10-97001275-C-T		not specified	Uncertain significance (Jan 23, 2023)
10-97001315-G-T		not specified	Uncertain significance (Jan 24, 2024)
10-97001324-G-A		not specified	Uncertain significance (Dec 05, 2022)
10-97002173-C-G		not specified	Uncertain significance (May 25, 2022)
10-97002201-G-C		not specified	Uncertain significance (Nov 09, 2021)
10-97002210-C-A		not specified	Uncertain significance (Aug 02, 2023)
10-97002235-C-T		not specified	Uncertain significance (Apr 07, 2023)
10-97002251-G-C		not specified	Uncertain significance (Feb 28, 2023)
10-97002253-C-T		not specified	Uncertain significance (Nov 09, 2021)
10-97002278-C-T		not specified	Uncertain significance (Mar 01, 2023)
10-97002279-G-A			Likely benign (Feb 01, 2023)
10-97002340-T-C		not specified	Uncertain significance (Feb 22, 2023)
10-97002341-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-97002342-G-A			Likely benign (Nov 01, 2022)
10-97002344-G-A		not specified	Uncertain significance (Feb 06, 2024)
10-97002350-C-G		not specified	Uncertain significance (Aug 12, 2021)
10-97002832-G-C		not specified	Uncertain significance (Jan 05, 2022)
10-97002959-C-T		not specified	Uncertain significance (Jul 27, 2021)
10-97004089-C-T		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLIT1	protein_coding	protein_coding	ENST00000266058	37	187883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000669	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.09	675	942	0.717	0.0000589	9991
Missense in Polyphen		259	457.07	0.56665		4935
Synonymous	2.01	352	403	0.873	0.0000267	2994
Loss of Function	7.26	11	81.9	0.134	0.00000407	910

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000458
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000234	0.000231
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions (By similarity). SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb. {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human);Spinal Cord Injury;Olfactory bulb development and olfactory learning;Developmental Biology;Regulation of commissural axon pathfinding by SLIT and ROBO;Posttranslational regulation of adherens junction stability and dissassembly;Netrin-1 signaling;Regulation of expression of SLITs and ROBOs;Signaling by ROBO receptors;Axon guidance;Regulation of cortical dendrite branching (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.130
• rvis_EVS: -2.03
• rvis_percentile_EVS: 1.7

Haploinsufficiency Scores

• pHI: 0.539
• hipred: Y
• hipred_score: 0.693
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.369

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slit1
• 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); 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: slit1b
• Affected structure: cranial nerve VIII
• Phenotype tag: abnormal
• Phenotype quality: defasciculated

Gene ontology

• Biological process: nuclear migration;axon guidance;motor neuron axon guidance;chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration;retinal ganglion cell axon guidance;dorsal/ventral axon guidance;axon extension involved in axon guidance;forebrain morphogenesis;negative chemotaxis;negative regulation of synapse assembly
• Cellular component: extracellular space;cell
• Molecular function: calcium ion binding;Roundabout binding