SLITRK4

SLIT and NTRK like family member 4, the group of SLIT and NTRK like family

Basic information

Region (hg38): X:143622790-143636101

Links

ENSG00000179542 ∙ NCBI:139065 ∙ OMIM:300562 ∙ HGNC:23502 ∙ Uniprot:Q8IW52 ∙ 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 SLITRK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLITRK4 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
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	1

Variants in SLITRK4

This is a list of pathogenic ClinVar variants found in the SLITRK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-143628770-C-T		not specified	Uncertain significance (Mar 03, 2025)
X-143628771-G-A		not specified	Uncertain significance (Nov 15, 2021)
X-143628892-T-G		not specified	Uncertain significance (Jan 03, 2024)
X-143628931-G-T		not specified	Uncertain significance (Jan 18, 2025)
X-143628933-C-A		not specified	Uncertain significance (Feb 27, 2025)
X-143628951-C-A		not specified	Uncertain significance (Dec 26, 2023)
X-143628969-G-A		not specified	Uncertain significance (May 01, 2024)
X-143629008-C-T		not specified	Uncertain significance (Jan 20, 2025)
X-143629050-T-C		not specified	Uncertain significance (Oct 17, 2024)
X-143629117-C-T		not specified	Uncertain significance (Nov 10, 2024)
X-143629118-A-G		not specified	Uncertain significance (Dec 31, 2023)
X-143629179-G-C		not specified	Uncertain significance (Dec 04, 2024)
X-143629322-G-A		not specified	Uncertain significance (Dec 28, 2022)
X-143629388-A-T		not specified	Uncertain significance (Nov 24, 2024)
X-143629406-T-C		not specified	Uncertain significance (Aug 26, 2024)
X-143629455-C-G		not specified	Uncertain significance (Jun 26, 2023)
X-143629567-G-A			Benign (Aug 16, 2017)
X-143629622-G-A		not specified	Uncertain significance (Aug 29, 2024)
X-143629713-C-T		not specified	Uncertain significance (Sep 04, 2024)
X-143629826-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-143629851-C-T		not specified	Uncertain significance (Apr 29, 2024)
X-143629880-C-T		not specified	Uncertain significance (Jan 03, 2024)
X-143629913-T-A		not specified	Uncertain significance (Nov 18, 2022)
X-143630009-T-A		not specified	Uncertain significance (Mar 25, 2024)
X-143630094-G-C		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLITRK4	protein_coding	protein_coding	ENST00000381779	1	13001

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.794	0.205	125713	2	2	125717	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	207	303	0.682	0.0000222	5507
Missense in Polyphen		68	135.8	0.50075		2561
Synonymous	1.09	111	127	0.877	0.00000972	1654
Loss of Function	3.33	3	18.4	0.163	0.00000160	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000762	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000245	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000528	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: It is involved in synaptogenesis and promotes synapse differentiation (PubMed:27812321). Suppresses neurite outgrowth (By similarity). {ECO:0000250|UniProtKB:Q810B8, ECO:0000269|PubMed:27812321}.
• Pathway: Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.251
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.588
• hipred: Y
• hipred_score: 0.707
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slitrk4
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype; immune system phenotype

Gene ontology

• Biological process: axonogenesis;regulation of synapse organization;positive regulation of synapse assembly
• Cellular component: plasma membrane;integral component of membrane;glutamatergic synapse