SLC6A9 solute carrier family 6 member 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC6A9provided by HGNC
Official Full Name: solute carrier family 6 member 9provided by HGNC
Primary source: HGNC:HGNC:11056
See related: Ensembl:ENSG00000196517 MIM:601019; AllianceGenome:HGNC:11056
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: GLYT1; GCENSG
Summary: The amino acid glycine acts as an inhibitory neurotransmitter in the central nervous system. The protein encoded by this gene is one of two transporters that stop glycine signaling by removing it from the synaptic cleft. [provided by RefSeq, Jun 2016]
Expression: Broad expression in skin (RPKM 13.4), adrenal (RPKM 9.7) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p34.1

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (43996483..44031462, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (43859929..43902553, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (44462155..44497134, complement)

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?

Transport mechanism and pharmacology of the human GlyT1.
Title: Transport mechanism and pharmacology of the human GlyT1.
Functional crosstalk of the glycine transporter GlyT1 and NMDA receptors.
Title: Functional crosstalk of the glycine transporter GlyT1 and NMDA receptors.
Structural insights into the inhibition of glycine reuptake.
Title: Structural insights into the inhibition of glycine reuptake.
Chloride-dependent conformational changes in the GlyT1 glycine transporter.
Title: Chloride-dependent conformational changes in the GlyT1 glycine transporter.
GlyT1 encephalopathy: Characterization of presumably disease causing GlyT1 mutations.
Title: GlyT1 encephalopathy: Characterization of presumably disease causing GlyT1 mutations.
GLYT1 encephalopathy: Further delineation of disease phenotype and discussion of pathophysiological mechanisms.
Title: GLYT1 encephalopathy: Further delineation of disease phenotype and discussion of pathophysiological mechanisms.
Do damaging variants of SLC6A9, the gene for the glycine transporter 1 (GlyT-1), protect against schizophrenia?
Title: Do damaging variants of SLC6A9, the gene for the glycine transporter 1 (GlyT-1), protect against schizophrenia?
Whole-exome sequencing revealed a novel homozygous missense variant in exon 9 of SLC6A9 NM_201649.3: c.1219 A>G (p.Ser407Gly) that segregates with the disease within the family. In murine model, knockout of Slc6a9 is associated with equivalent phenotype of non-ketotic hyperglycinemia (NKH), namely respiratory distress and hypotonia.
Title: Mutation in SLC6A9 encoding a glycine transporter causes a novel form of non-ketotic hyperglycinemia in humans.
This study demonstrates that lack of GLYT1 leads to a distinct human neurological syndrome hallmarked by mildly elevated cerebrospinal fluid glycine and normal serum glycine.
Title: Loss of Glycine Transporter 1 Causes a Subtype of Glycine Encephalopathy with Arthrogryposis and Mildly Elevated Cerebrospinal Fluid Glycine.
Study found that temporal lobe epilepsy is associated with increased levels of GlyT1
Title: Glycine transporter 1 is a target for the treatment of epilepsy.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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
Atypical glycine encephalopathy MedGen: C4310943 OMIM: 617301 GeneReviews: GLYT1 Encephalopathy	Compare labs

EBI GWAS Catalog

Description
Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families. 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

RH78692 (e-PCR)
- UniSTS:79664

RH70220 (e-PCR)
- UniSTS:70770

D1S2733 (e-PCR)
- UniSTS:72158

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables glycine transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables glycine transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables glycine:sodium symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycine:sodium symporter activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in glycine import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycine import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycine import across plasma membrane	TAS Traceable Author Statement more info	PubMed
involved_in glycine transport	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of negative regulation of NMDA glutamate receptor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in neurotransmitter transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of heme biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of hemoglobin biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic transmission, glycinergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic transmission, glycinergic	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 apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basal plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in dense core granule	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in hippocampal mossy fiber to CA3 synapse	IEA Inferred from Electronic Annotation more info
located_in lateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in parallel fiber to Purkinje cell synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sodium- and chloride-dependent glycine transporter 1

Names: glyT-1; solute carrier family 6 (neurotransmitter transporter, glycine), member 9

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.

Genomic

NG_050929.1 RefSeqGene

Range

5031..40010

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001024845.3 → NP_001020016.1 sodium- and chloride-dependent glycine transporter 1 isoform 3

See identical proteins and their annotated locations for NP_001020016.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 2. The resulting isoform (3) is shorter and has a distinct N-terminus compared to isoform 2. Variants 3 and 9 both encode the same isoform (3).

Source sequence(s)

AI884725, AL139220, CN354684, S70609

Consensus CDS

CCDS30695.1

UniProtKB/Swiss-Prot

P48067

Related

ENSP00000361384.4, ENST00000372310.8

Conserved Domains (1) summary

cd11498
Location:11 → 594

SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
NM_001261380.2 → NP_001248309.1 sodium- and chloride-dependent glycine transporter 1 isoform 4

See identical proteins and their annotated locations for NP_001248309.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region compared to variant 2. The resulting protein (isoform 4) is shorter compared to isoform 2.

Source sequence(s)

AK296438, AL139220, DA403430

UniProtKB/TrEMBL

B7Z3W8

Conserved Domains (1) summary

cd11498
Location:30 → 598

SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
NM_001328626.2 → NP_001315555.1 sodium- and chloride-dependent glycine transporter 1 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (5) is shorter at the N-terminus compared to isoform 2.

Source sequence(s)

AL139220

Consensus CDS

CCDS85966.1

UniProtKB/TrEMBL

B7Z589

Related

ENSP00000434460.1, ENST00000475075.6

Conserved Domains (1) summary

cl00456
Location:1 → 483

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001328627.1 → NP_001315556.1 sodium- and chloride-dependent glycine transporter 1 isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an alternate exon in the 5' end compared to variant 2. The resulting isoform (6) has a shorter and distinct N-terminus compared to isoform 2.

Source sequence(s)

AL139220

Conserved Domains (1) summary

cl00456
Location:42 → 573

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001328628.1 → NP_001315557.1 sodium- and chloride-dependent glycine transporter 1 isoform 7

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks two alternate exons in the 5' end compared to variant 2. The resulting isoform (7) has a shorter and distinct N-terminus compared to isoform 2.

Source sequence(s)

AL139220

Conserved Domains (1) summary

cl00456
Location:30 → 529

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001328629.1 → NP_001315558.1 sodium- and chloride-dependent glycine transporter 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (9) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 2. Variants 3 and 9 both encode the same isoform (3).

Source sequence(s)

AL139220

Consensus CDS

CCDS30695.1

UniProtKB/Swiss-Prot

P48067

Related

ENSP00000501314.1, ENST00000673836.1

Conserved Domains (1) summary

cd11498
Location:11 → 594

SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
NM_001328630.2 → NP_001315559.1 sodium- and chloride-dependent glycine transporter 1 isoform 8

Status: REVIEWED

Description

Transcript Variant: This variant (10) differs in the 5' UTR and coding sequence and lacks an alternate 3' in-frame exon compared to variant 2. The resulting isoform (8) is shorter at the N-terminus and lacks an alternate C-terminal segment compared to isoform 2.

Source sequence(s)

AL139220
NM_006934.4 → NP_008865.2 sodium- and chloride-dependent glycine transporter 1 isoform 1

See identical proteins and their annotated locations for NP_008865.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 2. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 2.

Source sequence(s)

AI884725, AL139220, S70612

Consensus CDS

CCDS41316.1

UniProtKB/Swiss-Prot

P48067

Related

ENSP00000350362.2, ENST00000357730.6

Conserved Domains (1) summary

cd11498
Location:30 → 613

SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
NM_201649.4 → NP_964012.2 sodium- and chloride-dependent glycine transporter 1 isoform 2

See identical proteins and their annotated locations for NP_964012.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).

Source sequence(s)

AI884725, AL139220, S70609

Consensus CDS

CCDS41317.1

UniProtKB/Swiss-Prot

A6NDH1, A6NII2, A6NNZ8, P48067, Q5TAB8, Q5TAB9, Q5TAC0

Related

ENSP00000353791.2, ENST00000360584.6

Conserved Domains (1) summary

cd11498
Location:84 → 667

SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain

RNA

NR_048548.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate 5' exon compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK315233, AL139220

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

43996483..44031462 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047428739.1 → XP_047284695.1 sodium- and chloride-dependent glycine transporter 1 isoform X1
XM_047428740.1 → XP_047284696.1 sodium- and chloride-dependent glycine transporter 1 isoform X2
XM_017002152.3 → XP_016857641.1 sodium- and chloride-dependent glycine transporter 1 isoform X4
XM_047428744.1 → XP_047284700.1 sodium- and chloride-dependent glycine transporter 1 isoform X6

Related

ENSP00000361380.3, ENST00000372306.7
XM_047428743.1 → XP_047284699.1 sodium- and chloride-dependent glycine transporter 1 isoform X5
XM_011542017.3 → XP_011540319.1 sodium- and chloride-dependent glycine transporter 1 isoform X3

Conserved Domains (1) summary

cl00456
Location:84 → 585

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

43859929..43902553 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338436.1 → XP_054194411.1 sodium- and chloride-dependent glycine transporter 1 isoform X10
XM_054338437.1 → XP_054194412.1 sodium- and chloride-dependent glycine transporter 1 isoform X10
XM_054338430.1 → XP_054194405.1 sodium- and chloride-dependent glycine transporter 1 isoform X8
XM_054338443.1 → XP_054194418.1 sodium- and chloride-dependent glycine transporter 1 isoform X12

UniProtKB/TrEMBL

B7Z3A9
XM_054338435.1 → XP_054194410.1 sodium- and chloride-dependent glycine transporter 1 isoform X10
XM_054338431.1 → XP_054194406.1 sodium- and chloride-dependent glycine transporter 1 isoform X8
XM_054338432.1 → XP_054194407.1 sodium- and chloride-dependent glycine transporter 1 isoform X8
XM_054338440.1 → XP_054194415.1 sodium- and chloride-dependent glycine transporter 1 isoform X11
XM_054338434.1 → XP_054194409.1 sodium- and chloride-dependent glycine transporter 1 isoform X9
XM_054338429.1 → XP_054194404.1 sodium- and chloride-dependent glycine transporter 1 isoform X7
XM_054338433.1 → XP_054194408.1 sodium- and chloride-dependent glycine transporter 1 isoform X1
XM_054338438.1 → XP_054194413.1 sodium- and chloride-dependent glycine transporter 1 isoform X2
XM_054338441.1 → XP_054194416.1 sodium- and chloride-dependent glycine transporter 1 isoform X4
XM_054338444.1 → XP_054194419.1 sodium- and chloride-dependent glycine transporter 1 isoform X6
XM_054338442.1 → XP_054194417.1 sodium- and chloride-dependent glycine transporter 1 isoform X5
XM_054338439.1 → XP_054194414.1 sodium- and chloride-dependent glycine transporter 1 isoform X3