SLC15A4 solute carrier family 15 member 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC15A4provided by HGNC
Official Full Name: solute carrier family 15 member 4provided by HGNC
Primary source: HGNC:HGNC:23090
See related: Ensembl:ENSG00000139370 MIM:615806; AllianceGenome:HGNC:23090
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PHT1; PTR4; FP12591
Summary: Enables L-histidine transmembrane transporter activity; peptide transmembrane transporter activity; and peptidoglycan transmembrane transporter activity. Involved in several processes, including dipeptide import across plasma membrane; peptidoglycan transport; and positive regulation of toll-like receptor signaling pathway. Located in endolysosome membrane. Is integral component of lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in bone marrow (RPKM 17.6), testis (RPKM 10.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.33

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (128793194..128823958, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (128825188..128855979, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (129277739..129308503, complement)

Chromosome 12 - NC_000012.12 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?

Oligopeptide/Histidine Transporter PHT1 and PHT2 - Function, Regulation, and Pathophysiological Implications Specifically in Immunoregulation.
Title: Oligopeptide/Histidine Transporter PHT1 and PHT2 - Function, Regulation, and Pathophysiological Implications Specifically in Immunoregulation.
Structural basis for recruitment of TASL by SLC15A4 in human endolysosomal TLR signaling.
Title: Structural basis for recruitment of TASL by SLC15A4 in human endolysosomal TLR signaling.
A conformation-locking inhibitor of SLC15A4 with TASL proteostatic anti-inflammatory activity.
Title: A conformation-locking inhibitor of SLC15A4 with TASL proteostatic anti-inflammatory activity.
Identification of SLC15A4/PHT1 Gene Products Upregulation Marking the Intestinal Epithelial Monolayer of Ulcerative Colitis Patients.
Title: Identification of SLC15A4/PHT1 Gene Products Upregulation Marking the Intestinal Epithelial Monolayer of Ulcerative Colitis Patients.
Whole exome sequencing identifies novel germline variants of SLC15A4 gene as potentially cancer predisposing in familial colorectal cancer.
Title: Whole exome sequencing identifies novel germline variants of SLC15A4 gene as potentially cancer predisposing in familial colorectal cancer.
Human SLC15A4 is crucial for TLR-mediated type I interferon production and mitochondrial integrity.
Title: Human SLC15A4 is crucial for TLR-mediated type I interferon production and mitochondrial integrity.
identification of TASL as the component that links endolysosomal TLRs to the IRF5 transcription factor via SLC15A4 provides a mechanistic explanation for the involvement of these proteins in systemic lupus erythematosus
Title: TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7-9.
The transporters PEPT2, PHT1, and PHT2 are responsible for the uptake of carnosine into glioblastoma cells and full function of all three transporters is required for maximum uptake.
Title: The proton-coupled oligopeptide transporters PEPT2, PHT1 and PHT2 mediate the uptake of carnosine in glioblastoma cells.
Study established a novel cell model to evaluate the function of hPHT1 in vitro and confirmed that muramyl peptide and Tri-DAP were substrates of hPHT1.
Title: Functional Characterization of Human Peptide/Histidine Transporter 1 in Stably Transfected MDCK Cells.
Targeted sequencing of two candidate genes, SLC20A1 and SLC15A4, of the solute carrier membrane transport protein family in 200 additional patients demonstrated two further variants predicted as damaging for combined hormone deficiency.
Title: Identification of SLC20A1 and SLC15A4 among other genes as potential risk factors for combined pituitary hormone deficiency.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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

EBI GWAS Catalog

Description
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. 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

SGC30248 (e-PCR)
- UniSTS:40568

RH102313 (e-PCR)
- UniSTS:96647

SGC31722 (e-PCR)
- UniSTS:17114

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-histidine transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables L-histidine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables dipeptide transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables dipeptide transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables peptide:proton symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables peptide:proton symporter activity	TAS Traceable Author Statement more info
enables peptidoglycan transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in L-histidine transmembrane export from vacuole	IEA Inferred from Electronic Annotation more info
involved_in dipeptide import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in dipeptide import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in histidine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in mast cell homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in monoatomic ion transport	TAS Traceable Author Statement more info
involved_in peptide transport	IEA Inferred from Electronic Annotation more info
involved_in peptidoglycan transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of toll-like receptor 7 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of toll-like receptor 8 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of toll-like receptor 9 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in proton transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of isotype switching to IgG isotypes	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in endolysosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in specific granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: solute carrier family 15 member 4

Names: hPHT1; peptide transporter 4; peptide-histidine transporter 4; peptide/histidine transporter 1; solute carrier family 15 (oligopeptide transporter), member 4

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.

mRNA and Protein(s)

NM_145648.4 → NP_663623.1 solute carrier family 15 member 4

See identical proteins and their annotated locations for NP_663623.1

Status: VALIDATED

Source sequence(s)

AC108704

Consensus CDS

CCDS9264.1

UniProtKB/Swiss-Prot

A6H8Y9, B3KTK1, Q71M34, Q7Z5F8, Q8N697, Q8TAH0

Related

ENSP00000266771.5, ENST00000266771.10

Conserved Domains (2) summary

pfam00854
Location:146 → 491

PTR2; POT family

cl21472
Location:40 → 247

MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

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_000012.12 Reference GRCh38.p14 Primary Assembly

Range

128793194..128823958 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011537895.2 → XP_011536197.1 solute carrier family 15 member 4 isoform X1

Conserved Domains (1) summary

pfam00854
Location:146 → 541

PTR2; POT family
XM_047428283.1 → XP_047284239.1 solute carrier family 15 member 4 isoform X2

UniProtKB/TrEMBL

H7BYB7

Related

ENSP00000365935.4, ENST00000376744.8

RNA

XR_007063044.1 RNA Sequence
XR_007063043.1 RNA Sequence
XR_007063045.1 RNA Sequence
XR_007063046.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

128825188..128855979 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054371064.1 → XP_054227039.1 solute carrier family 15 member 4 isoform X1
XM_054371065.1 → XP_054227040.1 solute carrier family 15 member 4 isoform X2

UniProtKB/TrEMBL

H7BYB7