SLC6A17

Chr 1AR

solute carrier family 6 member 17

Also known as: MRT48, NTT4

NCBI Gene: 388662ENSG00000197106UniProt: Q9H1V8OMIM: 610299

The protein is a synaptic vesicle transporter that uptakes neutral amino acids including proline, glycine, leucine and alanine in a sodium-coupled, proton gradient-driven mechanism, contributing to neurotransmitter precursor availability. Mutations cause autosomal recessive intellectual developmental disorder. The gene shows high constraint against loss-of-function variants (LOEUF 0.42), with strongest expression in cortical and hippocampal brain regions during development.

OMIMResearchSummary from RefSeq, OMIM, UniProt
MultiplemechanismARLOEUF 0.421 OMIM phenotype
Clinical Summary— SLC6A17
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Gene-Disease Validity (ClinGen)
progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome · ARModerate

Moderate evidence — consider for supplementary testing

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Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.50) — some intolerance to loss-of-function variants.
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ClinVar Variants
18 unique Pathogenic / Likely Pathogenic· 97 VUS of 162 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.42LOEUF
pLI 0.504
Z-score 3.86
OE 0.21 (0.12–0.42)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
2.39Z-score
OE missense 0.69 (0.62–0.75)
313 obs / 456.4 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.21 (0.12–0.42)
0≤0.351.4
Missense OE0.69 (0.62–0.75)
0≤0.61.4
Synonymous OE0.91
0≤1.21.6
LoF obs/exp: 6 / 28.0Missense obs/exp: 313 / 456.4Syn Z: 1.05
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongSLC6A17-related intellectual developmental disorderOTHERAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6357th %ile
GOF
0.81top 10%
LOF
0.3164th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

162 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic16
Likely Pathogenic2
VUS97
Likely Benign27
Benign8
Conflicting4
16
Pathogenic
2
Likely Pathogenic
97
VUS
27
Likely Benign
8
Benign
4
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
2
14
0
16
Likely Pathogenic
0
0
2
0
2
VUS
2
92
3
0
97
Likely Benign
0
5
0
22
27
Benign
0
2
1
5
8
Conflicting
—4
Total21012027154

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC6A17 · 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.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 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