SLITRK3

SLIT and NTRK like family member 3, the group of SLIT and NTRK like family

Basic information

Region (hg38): 3:165186720-165197109

Links

ENSG00000121871 ∙ NCBI:22865 ∙ OMIM:609679 ∙ HGNC:23501 ∙ Uniprot:O94933 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy (Limited), mode of inheritance: AD
• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLITRK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLITRK3 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			61	2		63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	3	1

Variants in SLITRK3

This is a list of pathogenic ClinVar variants found in the SLITRK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-165187929-C-T		not specified	Uncertain significance (Mar 07, 2023)
3-165187941-G-T		not specified	Uncertain significance (Jul 27, 2024)
3-165187943-T-A		not specified	Uncertain significance (Jan 09, 2024)
3-165187953-G-C		not specified	Uncertain significance (Sep 28, 2021)
3-165187989-T-C		not specified	Uncertain significance (Aug 23, 2021)
3-165188000-G-C		not specified	Uncertain significance (May 30, 2022)
3-165188001-T-C		not specified	Uncertain significance (Mar 23, 2022)
3-165188012-C-T		not specified	Uncertain significance (Jan 24, 2024)
3-165188018-G-A		not specified	Uncertain significance (Sep 15, 2021)
3-165188025-G-C		not specified	Uncertain significance (Jan 21, 2025)
3-165188132-A-G		not specified	Uncertain significance (Aug 13, 2021)
3-165188155-A-G			Benign (Dec 31, 2019)
3-165188163-G-T		not specified	Uncertain significance (Mar 29, 2022)
3-165188171-C-T		not specified	Uncertain significance (Aug 04, 2022)
3-165188232-C-A		not specified	Uncertain significance (Feb 10, 2023)
3-165188246-T-G		not specified	Uncertain significance (Jan 31, 2025)
3-165188249-C-T		not specified	Uncertain significance (Sep 01, 2021)
3-165188258-G-A		not specified	Uncertain significance (Feb 22, 2023)
3-165188267-C-A		not specified	Uncertain significance (Sep 09, 2024)
3-165188295-C-G		not specified	Uncertain significance (Apr 18, 2023)
3-165188348-T-C		not specified	Uncertain significance (Apr 05, 2023)
3-165188477-G-A		not specified	Uncertain significance (Aug 20, 2023)
3-165188532-A-T			Likely benign (Jan 01, 2023)
3-165188596-G-C		not specified	Uncertain significance (Apr 23, 2024)
3-165188620-A-G			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLITRK3	protein_coding	protein_coding	ENST00000475390	1	10390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.939	0.0609	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.589	489	527	0.928	0.0000279	6370
Missense in Polyphen		127	204.14	0.62213		2620
Synonymous	-1.84	240	206	1.16	0.0000108	2024
Loss of Function	4.32	5	30.9	0.162	0.00000203	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000270
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000703	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Suppresses neurite outgrowth. {ECO:0000250}.
• Pathway: Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.165
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.624
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slitrk3
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: axonogenesis;positive regulation of synapse assembly;synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: plasma membrane;GABA-ergic synapse;integral component of postsynaptic specialization membrane;integral component of postsynaptic density membrane