SLITRK6

SLIT and NTRK like family member 6, the group of SLIT and NTRK like family

Basic information

Region (hg38): 13:85792789-85806683

Links

ENSG00000184564 ∙ NCBI:84189 ∙ OMIM:609681 ∙ HGNC:23503 ∙ Uniprot:Q9H5Y7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• high myopia-sensorineural deafness syndrome (Strong), mode of inheritance: AR
• high myopia-sensorineural deafness syndrome (Strong), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• high myopia-sensorineural deafness syndrome (Supportive), mode of inheritance: AR
• high myopia-sensorineural deafness syndrome (Moderate), mode of inheritance: AR
• high myopia-sensorineural deafness syndrome (Definitive), mode of inheritance: AR
• high myopia-sensorineural deafness syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness and myopia	AR	Audiologic/Otolaryngologic	Awareness of prelingual hearing loss may allow early interventions related to speech and language development	Audiologic/Otolaryngologic; Ophthalmologic	23543054; 23946138

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLITRK6 gene.

• Global developmental delay (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLITRK6 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	41	6	48
missense			107	9	2	118
nonsense	1	5				6
start loss	1					1
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	7	10
Total	2	5	110	53	15

Variants in SLITRK6

This is a list of pathogenic ClinVar variants found in the SLITRK6 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-85793742-T-C			Benign (Nov 12, 2018)
13-85793838-CT-C			Benign (Nov 12, 2018)
13-85793850-C-CT			Benign (Aug 13, 2019)
13-85793985-A-G			Uncertain significance (Jan 31, 2022)
13-85793986-T-C			Likely benign (Aug 02, 2022)
13-85793990-T-C		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)
13-85794003-C-G		not specified • Inborn genetic diseases	Uncertain significance (Apr 04, 2024)
13-85794042-G-A			Uncertain significance (Aug 16, 2021)
13-85794056-T-C		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
13-85794060-T-C		Inborn genetic diseases	Uncertain significance (Jan 12, 2024)
13-85794089-C-T		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
13-85794090-G-A		SLITRK6-related disorder	Likely benign (Oct 13, 2023)
13-85794095-T-C		not specified	Uncertain significance (Aug 14, 2019)
13-85794096-A-G		High myopia-sensorineural deafness syndrome • Inborn genetic diseases	Uncertain significance (Apr 21, 2023)
13-85794104-G-A			Uncertain significance (Mar 28, 2022)
13-85794111-T-C			Likely benign (Jun 15, 2021)
13-85794127-G-A			Likely benign (May 01, 2022)
13-85794156-C-G		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
13-85794166-C-A			Likely benign (Sep 08, 2023)
13-85794195-T-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
13-85794196-G-A			Likely benign (Jul 17, 2023)
13-85794248-G-A		High myopia-sensorineural deafness syndrome	Uncertain significance (Jan 17, 2022)
13-85794265-G-T			Likely benign (Sep 29, 2022)
13-85794285-G-C			Uncertain significance (Aug 12, 2022)
13-85794287-T-G		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLITRK6	protein_coding	protein_coding	ENST00000400286	1	6699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.70e-14	0.0556	124682	0	69	124751	0.000277

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.381	456	434	1.05	0.0000213	5526
Missense in Polyphen		145	144.94	1.0004		1985
Synonymous	-2.07	198	164	1.21	0.00000835	1648
Loss of Function	0.511	22	24.7	0.889	0.00000142	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000612	0.000608
Ashkenazi Jewish	0.0000999	0.0000993
East Asian	0.000335	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.000302	0.000300
Middle Eastern	0.000335	0.000334
South Asian	0.000327	0.000327
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of neurite outgrowth required for normal hearing and vision. {ECO:0000269|PubMed:23543054}.
• Pathway: Neuronal System;EGFR1;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.820
• rvis_EVS: -0.78
• rvis_percentile_EVS: 13.05

Haploinsufficiency Scores

• pHI: 0.376
• hipred: N
• hipred_score: 0.251
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slitrk6
• Phenotype: hearing/vestibular/ear 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); growth/size/body region phenotype

Gene ontology

• Biological process: startle response;lens development in camera-type eye;auditory receptor cell morphogenesis;axonogenesis;synapse assembly;visual perception;sensory perception of sound;adult locomotory behavior;vestibulocochlear nerve development;auditory behavior;multicellular organism growth;positive regulation of synapse assembly;linear vestibuloocular reflex;innervation;cochlea development
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface