SLITRK2

SLIT and NTRK like family member 2, the group of SLIT and NTRK like family

Basic information

Region (hg38): X:145817829-145829856

Previous symbols: [ "SLITL1", "TMEM257", "CXorf1" ]

Links

ENSG00000185985 ∙ NCBI:84631 ∙ OMIM:300561 ∙ HGNC:13449 ∙ Uniprot:Q9H156 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder, X-linked 111 (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 111	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	35840571

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLITRK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLITRK2 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				7	2	9
missense			36			36
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	7	2

Variants in SLITRK2

This is a list of pathogenic ClinVar variants found in the SLITRK2 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-145822434-C-A		not specified	Uncertain significance (Feb 03, 2023)
X-145822435-G-A		not specified	Uncertain significance (Jun 11, 2021)
X-145822450-A-G		not specified	Uncertain significance (Apr 07, 2022)
X-145822462-G-A		not specified	Uncertain significance (Jan 26, 2022)
X-145822480-A-G		not specified	Uncertain significance (Apr 12, 2024)
X-145822499-C-T		not specified	Uncertain significance (Mar 18, 2024)
X-145822606-C-A		not specified	Uncertain significance (Feb 28, 2025)
X-145822646-T-C		Intellectual disability	Likely pathogenic (Jan 24, 2022)
X-145822663-A-G		not specified	Uncertain significance (Aug 08, 2023)
X-145822674-C-G			Likely benign (Feb 01, 2023)
X-145822709-A-G		not specified	Uncertain significance (Nov 09, 2024)
X-145822769-T-C		not specified	Uncertain significance (Jan 01, 2025)
X-145822828-A-T		not specified	Uncertain significance (May 30, 2024)
X-145822865-G-T		not specified	Uncertain significance (Mar 11, 2024)
X-145822960-C-T		not specified	Uncertain significance (Mar 04, 2025)
X-145823009-T-C		not specified	Uncertain significance (Jul 12, 2023)
X-145823026-G-A		not specified	Uncertain significance (Aug 19, 2024)
X-145823044-G-A		not specified	Uncertain significance (Oct 01, 2024)
X-145823053-G-A		Intellectual disability • Intellectual developmental disorder, X-linked 111	Conflicting classifications of pathogenicity (May 04, 2023)
X-145823055-G-T		Intellectual developmental disorder, X-linked 111	Uncertain significance (Apr 23, 2024)
X-145823129-C-T		not specified	Uncertain significance (Feb 12, 2025)
X-145823218-A-G		not specified	Uncertain significance (Feb 08, 2025)
X-145823246-G-A		not specified	Uncertain significance (Dec 27, 2023)
X-145823294-A-G		not specified	Uncertain significance (Jun 17, 2024)
X-145823311-A-G		not specified	Uncertain significance (Jul 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLITRK2	protein_coding	protein_coding	ENST00000370490	1	8011

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00641	0.990	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	212	323	0.656	0.0000247	5528
Missense in Polyphen		50	118.15	0.4232		2176
Synonymous	-0.725	150	139	1.08	0.0000112	1724
Loss of Function	2.54	7	18.9	0.370	0.00000164	315

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: It is involved in synaptogenesis and promotes excitatory synapse differentiation (PubMed:27273464, PubMed:27812321). Suppresses neurite outgrowth (By similarity). {ECO:0000250|UniProtKB:Q810C0, ECO:0000269|PubMed:27273464, ECO:0000269|PubMed:27812321}.
• Pathway: Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.279
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.88

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.809
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slitrk2

Gene ontology

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