SLITRK5

protein-coding

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

Gene summary

Members of the SLITRK family, such as SLITRK5, are integral membrane proteins with 2 N-terminal leucine-rich repeat (LRR) domains similar to those of SLIT proteins (see SLIT1; MIM 603742). Most SLITRKs, including SLITRK5, also have C-terminal regions that share homology with neurotrophin receptors (see NTRK1; MIM 191315). SLITRKs are expressed predominantly in neural tissues and have neurite-modulating activity (Aruga et al., 2003 [PubMed 14557068]).[supplied by OMIM, Mar 2008]

Previous symbols:

LRRC11

MANE transcript

NM_001384609.1

Inheritance

—

ClinVar variants

P:1U:154B:13

Top phenotype

SLITRK5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr13:87,671,371-87,696,272

External References & Databases

Ensembl (ENSG00000165300)

Transcript & Mutation Effects

hg38 • Region Span ~24.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLITRK5 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 151

SLITRK5-related disorderTotal: 12

not providedTotal: 4

Autism spectrum disorderTotal: 2

Abnormal brain morphologyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001384609.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar	2 clinvar	8
missense		1 clinvar	152 clinvar	4 clinvar	1 clinvar	158
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	1	154	10	3	168

Highest pathogenic variant AF is 0.0000024795468

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001384609.1	RefSeq	NP_001371538.1	1	MANE Select
ENST00000683689.1	Ensembl	ENSP00000508338.1	1	MANE Select
NM_001384610.1	RefSeq	NP_001371539.1	1	Standard
NM_015567.2	RefSeq	NP_056382.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuronal System
Receptor-type tyrosine-protein phosphatases
Protein-protein interactions at synapses

Biological Process

chemical synaptic transmission
axonogenesis
grooming behavior
response to xenobiotic stimulus
striatum development

Cellular Component

plasma membrane
integral component of membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325089
Coding exons: 1
Length: 7002
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0532	546	550	0.994	0.0000313	6249
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000074	0.000062	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Suppresses neurite outgrowth. {ECO:0000250}.;

Recessive Scores

pRec: 0.122

Intolerance Scores

LoFtool: 0.101
RVIS EVS: -1.64
RVIS percentile EVS: 2.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.421

Gene Damage Prediction

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