SLITRK5

SLIT and NTRK like family member 5, the group of SLIT and NTRK like family

Basic information

Region (hg38): 13:87671371-87696272

Previous symbols: [ "LRRC11" ]

Links

ENSG00000165300 ∙ NCBI:26050 ∙ OMIM:609680 ∙ HGNC:20295 ∙ Uniprot:O94991 ∙ 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 SLITRK5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLITRK5 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	2	6
missense		1	55	2	1	59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	55	6	3

Variants in SLITRK5

This is a list of pathogenic ClinVar variants found in the SLITRK5 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-87675407-C-T		not specified	Uncertain significance (Sep 27, 2021)
13-87675428-C-A		not specified	Uncertain significance (Aug 27, 2024)
13-87675474-C-T		not specified	Uncertain significance (Apr 24, 2024)
13-87675510-T-C		not specified	Uncertain significance (Aug 02, 2023)
13-87675514-T-G		not specified	Uncertain significance (Mar 20, 2023)
13-87675546-C-T		not specified	Uncertain significance (Sep 08, 2024)
13-87675563-G-T		Autism spectrum disorder	association (-)
13-87675579-G-C		not specified	Uncertain significance (Feb 10, 2023)
13-87675603-G-A		not specified	Uncertain significance (Aug 10, 2024)
13-87675635-A-G		not specified	Likely benign (Jun 02, 2024)
13-87675672-G-A		not specified	Uncertain significance (Nov 08, 2024)
13-87675684-A-G		not specified	Uncertain significance (Jan 09, 2024)
13-87675742-G-T		SLITRK5-related disorder	Likely benign (Sep 10, 2019)
13-87675829-T-G		not specified	Uncertain significance (Dec 27, 2023)
13-87675831-C-A		not specified	Uncertain significance (Aug 16, 2021)
13-87675863-C-G		not specified	Uncertain significance (Mar 28, 2024)
13-87675885-G-A		not specified	Uncertain significance (Nov 06, 2023)
13-87675896-C-T		not specified	Uncertain significance (Oct 20, 2023)
13-87675956-T-C		not specified	Uncertain significance (Nov 13, 2024)
13-87676011-G-A		not specified	Uncertain significance (Dec 31, 2023)
13-87676040-G-A		not specified	Uncertain significance (Nov 17, 2022)
13-87676193-C-G		not specified	Uncertain significance (Mar 01, 2023)
13-87676211-T-C			Likely benign (Mar 01, 2023)
13-87676216-C-A		not specified	Uncertain significance (Dec 21, 2022)
13-87676244-A-G		not specified	Uncertain significance (Oct 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLITRK5	protein_coding	protein_coding	ENST00000325089	1	7002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.870	0.130	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0532	546	550	0.994	0.0000313	6249
Missense in Polyphen		102	155.67	0.65524		1984
Synonymous	-3.08	313	251	1.25	0.0000154	2000
Loss of Function	3.81	4	24.3	0.165	0.00000123	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000133	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000368	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000163
Other	0.00	0.00

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: 0.122

Intolerance Scores

• loftool: 0.101
• rvis_EVS: -1.64
• rvis_percentile_EVS: 2.82

Haploinsufficiency Scores

• pHI: 0.340
• hipred: Y
• hipred_score: 0.837
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slitrk5
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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)

Gene ontology

• Biological process: chemical synaptic transmission;axonogenesis;grooming behavior;response to xenobiotic stimulus;striatum development;adult behavior;skin development;dendrite morphogenesis;positive regulation of synapse assembly;cardiovascular system development
• Cellular component: plasma membrane;integral component of membrane;receptor complex