SLC6A17 solute carrier family 6 member 17 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC6A17provided by HGNC
Official Full Name: solute carrier family 6 member 17provided by HGNC
Primary source: HGNC:HGNC:31399
See related: Ensembl:ENSG00000197106 MIM:610299; AllianceGenome:HGNC:31399
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NTT4; MRT48
Summary: The protein encoded by this gene is a member of the SLC6 family of transporters, which are responsible for the presynaptic uptake of most neurotransmitters. The encoded vesicular transporter is selective for proline, glycine, leucine and alanine. In mouse, the strongest expression of this gene was in cortical and hippocampal tissues where expression increased during embryonic brain development and peaked postnatally. Defects in this gene cause a form of autosomal recessive intellectual disability. [provided by RefSeq, Jul 2017]
Expression: Biased expression in brain (RPKM 23.3), adrenal (RPKM 2.5) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 1p13.3

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (110150494..110202202)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (110165448..110217172)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (110693116..110744824)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Our genetic findings implicate homozygous SLC6A17 mutations in autosomal-recessive intellectual disability.
Title: Homozygous SLC6A17 mutations cause autosomal-recessive intellectual disability with progressive tremor, speech impairment, and behavioral problems.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
The substrate profile of the NTT4/XT1-dependent activity is similar to that of the closely related B(0)AT2/SBAT1 (SLC6A15), including a submillimolar apparent affinity for proline and leucine and a low millimolar apparent affinity for glutamine.
Title: Synaptic Vesicle Protein NTT4/XT1 (SLC6A17) Catalyzes Na+-coupled Neutral Amino Acid Transport.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome MedGen: C4225395 OMIM: 616269 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SLC6A17__6853 (e-PCR)
- UniSTS:466451

SHGC-30398 (e-PCR)
- UniSTS:43043

D1S2695 (e-PCR), detects polymorphism
- UniSTS:52049

WI-9875 (e-PCR)
- UniSTS:146570

RH103098 (e-PCR)
- UniSTS:97432

G60557 (e-PCR)
- UniSTS:137663

RH94096 (e-PCR)
- UniSTS:85202

WI-19280 (e-PCR)
- UniSTS:38115

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables symporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in L-leucine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-leucine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in alanine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in alanine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in neurotransmitter transport	IEA Inferred from Electronic Annotation more info
involved_in neutral amino acid transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in proline transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in proline transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in transport across blood-brain barrier	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sodium-dependent neutral amino acid transporter SLC6A17

Names: neurotransmitter transporter 4; orphan sodium- and chloride-dependent neurotransmitter transporter NTT4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.