SLC15A3

gene
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Also known as PHT2hPTR3

Summary

SLC15A3 (solute carrier family 15 member 3, HGNC:18068) is a protein-coding gene on chromosome 11q12.2, encoding Solute carrier family 15 member 3 (Q8IY34). Proton-coupled amino-acid transporter that transports free histidine and certain di- and tripeptides, and is involved in innate immune response.

Enables dipeptide transmembrane transporter activity. Involved in dipeptide import across plasma membrane. Located in intracellular membrane-bounded organelle.

Source: NCBI Gene 51296 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 108 total
  • MANE Select transcript: NM_016582

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18068
Approved symbolSLC15A3
Namesolute carrier family 15 member 3
Location11q12.2
Locus typegene with protein product
StatusApproved
AliasesPHT2, hPTR3
Ensembl geneENSG00000110446
Ensembl biotypeprotein_coding
OMIM610408
Entrez51296

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 12 protein_coding, 4 retained_intron, 2 nonsense_mediated_decay

ENST00000227880, ENST00000536491, ENST00000536784, ENST00000537307, ENST00000538739, ENST00000540272, ENST00000541505, ENST00000543406, ENST00000544101, ENST00000679573, ENST00000681015, ENST00000681275, ENST00000681882, ENST00000681951, ENST00000930270, ENST00000930271, ENST00000952095, ENST00000952096

RefSeq mRNA: 1 — MANE Select: NM_016582 NM_016582

CCDS: CCDS7998

Canonical transcript exons

ENST00000227880 — 8 exons

ExonStartEnd
ENSE000008514486095099460952176
ENSE000016281946094112260941290
ENSE000024869646094368960943836
ENSE000025067736094203560942145
ENSE000035057256093708460937373
ENSE000036356336094653260946821
ENSE000036490386093948060939638
ENSE000036778546093787060938025

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 97.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.1394 / max 814.7836, expressed in 977 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter IDTPM avgSamples expressed
1199325.5579466
1199270.7500151
1199340.7163388
1199240.7098181
1199350.4822243
1199310.3666112
1199230.333195
1199280.3288100
1199300.2399103
1199290.223674

Top tissues by expression

271 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009497.33gold quality
monocyteCL:000057697.10gold quality
leukocyteCL:000073896.61gold quality
tibial nerveUBERON:000132396.59gold quality
mononuclear cellCL:000084296.54gold quality
upper lobe of left lungUBERON:000895296.47gold quality
right lungUBERON:000216796.23gold quality
spleenUBERON:000210696.05gold quality
apex of heartUBERON:000209895.41gold quality
upper lobe of lungUBERON:000894895.28gold quality
gall bladderUBERON:000211094.52gold quality
right ovaryUBERON:000211893.78gold quality
muscle layer of sigmoid colonUBERON:003580593.74gold quality
mucosa of stomachUBERON:000119993.56gold quality
right coronary arteryUBERON:000162593.18gold quality
left ovaryUBERON:000211993.17gold quality
omental fat padUBERON:001041492.80gold quality
peritoneumUBERON:000235892.72gold quality
lower esophagus muscularis layerUBERON:003583392.45gold quality
lower esophagusUBERON:001347392.43gold quality
left coronary arteryUBERON:000162692.26gold quality
vermiform appendixUBERON:000115492.22gold quality
esophagogastric junction muscularis propriaUBERON:003584192.12gold quality
bloodUBERON:000017891.92gold quality
small intestine Peyer’s patchUBERON:000345491.86gold quality
lymph nodeUBERON:000002991.74gold quality
left uterine tubeUBERON:000130391.65gold quality
adipose tissue of abdominal regionUBERON:000780891.56gold quality
endocervixUBERON:000045891.33gold quality
coronary arteryUBERON:000162191.13gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes22.77
E-MTAB-2983no341.37
E-MTAB-5061no3.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting SLC15A3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-449699.8868.892236
HSA-MIR-449299.8768.253611
HSA-MIR-76299.5866.611994
HSA-MIR-449899.4767.422360
HSA-MIR-210-5P98.5764.37832
HSA-MIR-365297.7165.431890
HSA-MIR-443097.4765.611813
HSA-MIR-4749-3P96.4066.24798

Literature-anchored findings (GeneRIF, showing 5)

  • PEPT1,PEPT2, PHT1, and PHT2 are expressed in human nasal epithelium. (PMID:21366347)
  • Our results demonstrate that SLC15A3 is induced by viral infection to participate in intracellular RNA and DNA receptor-mediated interferon production (PMID:30069489)
  • 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. (PMID:31073693)
  • Substrate Transport Properties of the Human Peptide/Histidine Transporter PHT2 in Transfected MDCK Cells. (PMID:31254495)
  • Oligopeptide/Histidine Transporter PHT1 and PHT2 - Function, Regulation, and Pathophysiological Implications Specifically in Immunoregulation. (PMID:37610621)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
mus_musculusSlc15a3ENSMUSG00000024737
rattus_norvegicusSlc15a3ENSRNOG00000021644
drosophila_melanogasterCG2930FBGN0028491
drosophila_melanogasterCG9444FBGN0037730
drosophila_melanogasteryinFBGN0265575
caenorhabditis_elegansWBGENE00003877

Paralogs (4): SLC15A1 (ENSG00000088386), SLC15A4 (ENSG00000139370), SLC15A2 (ENSG00000163406), SLC15A5 (ENSG00000188991)

Protein

Protein identifiers

Solute carrier family 15 member 3Q8IY34 (reviewed: Q8IY34)

Alternative names: Osteoclast transporter, Peptide transporter 3, Peptide/histidine transporter 2

All UniProt accessions (10): Q8IY34, A0A7P0T8B5, A0A7P0T8H0, A0A7P0TAX8, A0A7P0Z4G8, F5GZ36, F5H1C8, F5H251, H0YFC1, H0YG40

UniProt curated annotations — full annotation on UniProt →

Function. Proton-coupled amino-acid transporter that transports free histidine and certain di- and tripeptides, and is involved in innate immune response. Preferably binds to short peptides with a basic residue at the first position and a hydrophobic residue at the second position. Also able to transport carnosine. Involved in the detection of microbial pathogens by toll-like receptors (TLRs) and NOD-like receptors (NLRs), probably by mediating transport of bacterial peptidoglycans across the endolysosomal membrane: catalyzes the transport of certain bacterial peptidoglycans, such as muramyl dipeptide (MDP), the NOD2 ligand.

Subunit / interactions. May form a homodimer.

Subcellular location. Lysosome membrane. Endosome membrane.

Similarity. Belongs to the major facilitator superfamily. Proton-dependent oligopeptide transporter (POT/PTR) (TC 2.A.17) family.

RefSeq proteins (1): NP_057666* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000109POT_famFamily
IPR036259MFS_trans_sfHomologous_superfamily

Pfam: PF00854

Catalyzed reactions (Rhea), 4 shown:

  • N-acetyl-D-muramoyl-L-alanyl-D-isoglutamine(out) + n H(+)(out) = N-acetyl-D-muramoyl-L-alanyl-D-isoglutamine(in) + n H(+)(in) (RHEA:76371)
  • L-histidine(out) + n H(+)(out) = L-histidine(in) + n H(+)(in) (RHEA:76379)
  • carnosine(out) + n H(+)(out) = carnosine(in) + n H(+)(in) (RHEA:76383)
  • glycylglycylglycine(out) + n H(+)(out) = glycylglycylglycine(in) + n H(+)(in) (RHEA:76391)

UniProt features (59 total): helix 20, topological domain 13, transmembrane region 12, glycosylation site 5, strand 3, turn 2, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8WX2ELECTRON MICROSCOPY3.44
8ZATELECTRON MICROSCOPY3.54

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IY34-F180.880.42

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (5): 61, 66, 223, 356, 439

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-427975Proton/oligopeptide cotransporters
R-HSA-382551Transport of small molecules
R-HSA-425393
R-HSA-425407SLC-mediated transmembrane transport

MSigDB gene sets: 297 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOCC_VACUOLAR_MEMBRANE, GOBP_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_SIGNALING_PATHWAY, GOBP_MONOATOMIC_CATION_TRANSPORT, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOMF_PROTON_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, IRF_Q6, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, BROWN_MYELOID_CELL_DEVELOPMENT_UP, VALK_AML_CLUSTER_5

GO Biological Process (10): monoatomic ion transport (GO:0006811), protein transport (GO:0015031), peptidoglycan transport (GO:0015835), innate immune response (GO:0045087), positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434), dipeptide import across plasma membrane (GO:0140206), immune system process (GO:0002376), peptide transport (GO:0015833), transmembrane transport (GO:0055085), proton transmembrane transport (GO:1902600)

GO Molecular Function (6): peptide:proton symporter activity (GO:0015333), peptidoglycan transmembrane transporter activity (GO:0015647), dipeptide transmembrane transporter activity (GO:0071916), protein binding (GO:0005515), symporter activity (GO:0015293), transmembrane transporter activity (GO:0022857)

GO Cellular Component (5): lysosomal membrane (GO:0005765), endosome membrane (GO:0010008), lysosome (GO:0005764), endosome (GO:0005768), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
SLC-mediated transport of oligopeptides1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport4
dipeptide transmembrane transport2
intracellular protein localization1
establishment of protein localization1
nitrogen compound transport1
carbohydrate derivative transport1
immune response1
defense response to symbiont1
positive regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway1
nucleotide-binding oligomerization domain containing 2 signaling pathway1
regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway1
oligopeptide import across plasma membrane1
biological_process1
cellular process1
monoatomic cation transmembrane transport1
solute:proton symporter activity1
peptide transmembrane transporter activity1
peptidoglycan transport1
macromolecule transmembrane transporter activity1
carbohydrate derivative transmembrane transporter activity1
oligopeptide transmembrane transporter activity1
binding1
secondary active transmembrane transporter activity1
transporter activity1
transmembrane transport1
lysosome1
lytic vacuole membrane1
endosome1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
lytic vacuole1
endomembrane system1
cytoplasmic vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

1824 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC15A3CD6P30203783
SLC15A3CD5P06127640
SLC15A3CARNS1A5YM72528
SLC15A3SLC47A1Q96FL8429
SLC15A3SULT1A2P50226426
SLC15A3SLC6A6P31641418
SLC15A3SLC7A4O43246409
SLC15A3NOD1Q9Y239408
SLC15A3NOD2Q9HC29403
SLC15A3SLC38A5Q8WUX1402
SLC15A3OR6X1Q8NH79397
SLC15A3CNDP2Q96KP4367
SLC15A3SLC15A2Q16348354
SLC15A3SLC38A7Q9NVC3347
SLC15A3CNDP1Q96KN2342

IntAct

25 interactions, top by confidence:

ABTypeScore
KRTAP12-2SLC15A3psi-mi:“MI:0915”(physical association)0.600
SLC15A3KRTAP12-2psi-mi:“MI:0915”(physical association)0.600
SLC15A3MDFIpsi-mi:“MI:0915”(physical association)0.560
KRTAP5-9SLC15A3psi-mi:“MI:0915”(physical association)0.560
SLC15A3KRTAP9-8psi-mi:“MI:0915”(physical association)0.560
HOXA1SLC15A3psi-mi:“MI:0915”(physical association)0.560
KRTAP19-2SLC15A3psi-mi:“MI:0915”(physical association)0.560
SLC15A3NOD2psi-mi:“MI:0915”(physical association)0.400
SLC15A3SLC15A4psi-mi:“MI:0915”(physical association)0.400
SLC15A3GXYLT2psi-mi:“MI:0914”(association)0.350
SLC15A3MDFIpsi-mi:“MI:0915”(physical association)0.000
SLC15A3KRTAP5-9psi-mi:“MI:0915”(physical association)0.000
KRTAP12-2SLC15A3psi-mi:“MI:0915”(physical association)0.000
SLC15A3HOXA1psi-mi:“MI:0915”(physical association)0.000
SLC15A3KRTAP9-8psi-mi:“MI:0915”(physical association)0.000
SLC15A3KRTAP19-2psi-mi:“MI:0915”(physical association)0.000
SLC15A3KRTAP12-2psi-mi:“MI:0915”(physical association)0.000

BioGRID (414): SLC15A3 (Two-hybrid), SLC15A3 (Two-hybrid), SLC15A3 (Two-hybrid), SLC15A3 (Two-hybrid), GMCL1 (Two-hybrid), LZTS2 (Two-hybrid), KRTAP10-3 (Two-hybrid), ABCC1 (Affinity Capture-MS), ACAD9 (Affinity Capture-MS), ADAM10 (Affinity Capture-MS), ADCK4 (Affinity Capture-MS), AGPAT2 (Affinity Capture-MS), AIFM1 (Affinity Capture-MS), ALDH3A2 (Affinity Capture-MS), ALDOA (Affinity Capture-MS)

ESM2 similar proteins: A1A5Z0, A6NM10, F6S3G9, O19133, O42153, O42154, O62735, P34080, P35575, P35576, P41181, P43428, P51802, P56402, P58355, P79099, Q05B81, Q06393, Q0VC03, Q10M80, Q148G2, Q19KA1, Q29RU6, Q4LE88, Q5U2T1, Q6AZ83, Q6NSQ9, Q6RZ07, Q71B07, Q7ZVP8, Q866G7, Q8BHH1, Q8BMD6, Q8BPX9, Q8CHJ2, Q8CHM1, Q8IXF9, Q8IY34, Q8NBQ7, Q924V4

Diamond homologs: A6QQL0, O09014, Q68F72, Q8BPX9, Q8IY34, Q8N697, Q91W98, Q924V4, P91679, O01840

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

108 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance90
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1123 predictions. Top by Δscore:

VariantEffectΔscore
11:60937866:TCA:Tdonor_loss1.0000
11:60937867:CACCA:Cdonor_loss1.0000
11:60937868:A:ACdonor_gain1.0000
11:60937868:A:Tdonor_loss1.0000
11:60937869:C:CCdonor_gain1.0000
11:60937869:C:Tdonor_loss1.0000
11:60939474:GGGTA:Gdonor_loss1.0000
11:60939475:GGTAC:Gdonor_loss1.0000
11:60939476:GTACC:Gdonor_loss1.0000
11:60939477:TA:Tdonor_loss1.0000
11:60939478:A:AGdonor_loss1.0000
11:60939502:A:ACdonor_gain1.0000
11:60939503:C:CCdonor_gain1.0000
11:60939634:GACTC:Gacceptor_gain1.0000
11:60939636:CTC:Cacceptor_gain1.0000
11:60939637:TC:Tacceptor_gain1.0000
11:60939638:CC:Cacceptor_gain1.0000
11:60939639:C:CCacceptor_gain1.0000
11:60939639:CTGGT:Cacceptor_loss1.0000
11:60939642:G:Cacceptor_gain1.0000
11:60939642:G:GCacceptor_gain1.0000
11:60939651:C:CTacceptor_gain1.0000
11:60943684:CTCA:Cdonor_loss1.0000
11:60943685:TCA:Tdonor_loss1.0000
11:60943686:CAC:Cdonor_loss1.0000
11:60943687:A:ACdonor_gain1.0000
11:60943687:A:Tdonor_loss1.0000
11:60943688:C:CCdonor_gain1.0000
11:60943688:C:CTdonor_loss1.0000
11:60943837:C:CCacceptor_gain1.0000

AlphaMissense

3719 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:60939620:C:GR432P0.995
11:60939502:A:CS471R0.994
11:60939502:A:TS471R0.994
11:60939504:T:GS471R0.994
11:60939629:T:AE429V0.994
11:60939621:G:TR432S0.993
11:60942111:A:GL344P0.992
11:60937972:C:GG497R0.991
11:60938013:G:TA483D0.991
11:60939487:G:CS476R0.991
11:60939487:G:TS476R0.991
11:60939489:T:GS476R0.991
11:60941278:A:GW374R0.991
11:60941278:A:TW374R0.991
11:60938016:A:GF482S0.990
11:60951033:G:CS173R0.990
11:60951033:G:TS173R0.990
11:60951035:T:GS173R0.990
11:60951231:G:CS107R0.990
11:60951231:G:TS107R0.990
11:60951233:T:GS107R0.990
11:60937950:C:TG504E0.989
11:60942122:C:AQ340H0.989
11:60942122:C:GQ340H0.989
11:60939630:C:TE429K0.988
11:60946765:G:CS205R0.987
11:60946765:G:TS205R0.987
11:60946767:T:GS205R0.987
11:60937944:C:TG506D0.986
11:60939628:C:AE429D0.986

dbSNP variants (sampled 300 via entrez): RS1000073951 (11:60944643 T>C), RS1000239315 (11:60938416 T>C,G), RS1000377494 (11:60940713 A>G), RS1000901961 (11:60948621 C>T), RS1001007311 (11:60952386 AT>A,ATT), RS1001124587 (11:60952158 C>A,G,T), RS1001422974 (11:60939865 A>G), RS1001481018 (11:60943467 G>A), RS1001685647 (11:60946972 A>G), RS1001754682 (11:60938327 A>C,G), RS1002032320 (11:60944026 G>C), RS1002216677 (11:60953996 G>A), RS1002364085 (11:60948360 G>A), RS1002411402 (11:60951953 C>A), RS1002632140 (11:60942882 G>A)

Disease associations

OMIM: gene MIM:610408 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST006192_46Systolic blood pressure x smoking status (ever vs never) interaction (2df test)3.000000e-06
GCST006195_89Systolic blood pressure x smoking status (current vs non-current) interaction (2df test)3.000000e-09
GCST010002_239Refractive error2.000000e-24

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0006335systolic blood pressure
EFO:0006527smoking status measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC15 family of peptide transporters

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases mutagenesis, affects methylation, increases expression, increases methylation3
Air Pollutantsaffects expression, increases abundance, decreases expression2
Nickelincreases expression2
Valproic Acidaffects expression, increases methylation2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
di-n-butylphosphoric acidaffects expression1
entinostataffects cotreatment, increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
dorsomorphinincreases expression, affects cotreatment1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Temozolomideincreases expression1
Acetaminophendecreases expression1
Arbutindecreases expression1
Benzeneincreases expression1
Doxorubicindecreases expression1
Lipopolysaccharidesaffects response to substance, increases expression1
Ozoneaffects expression, increases abundance1
Dronabinoldecreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoinincreases expression1
Asbestos, Serpentinedecreases expression1
Antirheumatic Agentsdecreases expression1
Okadaic Acidincreases expression1
Particulate Matterincreases abundance, decreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1HKAbcam A-549 SLC15A3 KOCancer cell lineMale
CVCL_E0NKUbigene HeLa SLC15A3 KOCancer cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.