SLITRK1

Chr 13ADMulti

SLIT and NTRK like family member 1

Also known as: LRRC12, TTM

NCBI Gene: 114798ENSG00000178235UniProt: Q96PX8OMIM: 609678

SLITRK1 encodes an integral membrane protein with leucine-rich repeat domains that promotes excitatory synapse differentiation and enhances neuronal dendrite outgrowth. Mutations cause Tourette syndrome and possibly trichotillomania, with autosomal dominant and multifactorial inheritance patterns. The gene is highly constrained against loss-of-function variants (pLI 0.96, LOEUF 0.34), indicating that complete protein loss is likely not tolerated.

OMIMResearchSummary from RefSeq, OMIM, UniProt
AD/MultiLOEUF 0.342 OMIM phenotypes
Clinical Summary— SLITRK1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.96). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
82 unique Pathogenic / Likely Pathogenic· 165 VUS of 260 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.34LOEUF
pLI 0.957
Z-score 3.58
OE 0.11 (0.04–0.34)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
0.41Z-score
OE missense 0.94 (0.86–1.03)
329 obs / 350.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.11 (0.04–0.34)
0≤0.351.4
Missense OE0.94 (0.86–1.03)
0≤0.61.4
Synonymous OE1.18
0≤1.21.6
LoF obs/exp: 2 / 18.7Missense obs/exp: 329 / 350.3Syn Z: -1.77

ClinVar Variant Classifications

260 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic82
VUS165
Likely Benign10
Benign1
Conflicting2
82
Pathogenic
165
VUS
10
Likely Benign
1
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
81
0
82
Likely Pathogenic
0
0
0
0
0
VUS
0
91
66
8
165
Likely Benign
0
2
6
2
10
Benign
0
0
0
1
1
Conflicting
—2
Total19315311260

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLITRK1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients