SLC15A5

Summary

SLC15A5 (solute carrier family 15 member 5, HGNC:33455) is a protein-coding gene on chromosome 12p12.3, encoding Solute carrier family 15 member 5 (A6NIM6). Proton oligopeptide cotransporter.

Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be active in membrane.

Source: NCBI Gene 729025 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_001170798

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33455
Approved symbol	SLC15A5
Name	solute carrier family 15 member 5
Location	12p12.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000188991
Ensembl biotype	protein_coding
OMIM	620324
Entrez	729025

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000344941

RefSeq mRNA: 1 — MANE Select: NM_001170798 NM_001170798

Canonical transcript exons

ENST00000344941 — 9 exons

Exon	Start	End
ENSE00001366788	16194345	16194453
ENSE00001372575	16216893	16217024
ENSE00001374776	16272561	16272783
ENSE00001376927	16257701	16257870
ENSE00001377618	16224414	16224602
ENSE00001384369	16244580	16244800
ENSE00001385851	16188485	16189815
ENSE00001391252	16239681	16239867
ENSE00001799951	16277325	16277685

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 77.04.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.04	gold quality
cortical plate	UBERON:0005343	46.98	gold quality
substantia nigra	UBERON:0002038	45.51	gold quality
prefrontal cortex	UBERON:0000451	45.09	gold quality
amygdala	UBERON:0001876	43.86	gold quality
temporal lobe	UBERON:0001871	43.66	gold quality
hypothalamus	UBERON:0001898	41.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	41.18	silver quality
caudate nucleus	UBERON:0001873	40.21	gold quality
frontal cortex	UBERON:0001870	40.10	gold quality
adipose tissue	UBERON:0001013	40.02	gold quality
subcutaneous adipose tissue	UBERON:0002190	39.93	gold quality
omental fat pad	UBERON:0010414	39.72	gold quality
sural nerve	UBERON:0015488	39.66	gold quality
nucleus accumbens	UBERON:0001882	39.29	silver quality
cerebral cortex	UBERON:0000956	38.80	gold quality
bone marrow cell	CL:0002092	38.54	gold quality
putamen	UBERON:0001874	38.32	gold quality
anterior cingulate cortex	UBERON:0009835	38.30	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	37.78	silver quality
Ammon’s horn	UBERON:0001954	37.77	gold quality
brain	UBERON:0000955	37.37	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
liver	UBERON:0002107	36.39	gold quality
superior frontal gyrus	UBERON:0002661	35.60	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
endometrium	UBERON:0001295	34.74	gold quality
granulocyte	CL:0000094	34.46	gold quality
right lobe of liver	UBERON:0001114	34.43	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.92
E-HCAD-30	no	35.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting SLC15A5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc15a5	ENSDARG00000089974
mus_musculus	Slc15a5	ENSMUSG00000044378
rattus_norvegicus	Slc15a5	ENSRNOG00000007717

Paralogs (4): SLC15A1 (ENSG00000088386), SLC15A3 (ENSG00000110446), SLC15A4 (ENSG00000139370), SLC15A2 (ENSG00000163406)

Protein

Protein identifiers

Solute carrier family 15 member 5 — A6NIM6 (reviewed: A6NIM6)

All UniProt accessions (1): A6NIM6

UniProt curated annotations — full annotation on UniProt →

Function. Proton oligopeptide cotransporter.

Subcellular location. Membrane.

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

RefSeq proteins (1): NP_001164269* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000109	POT_fam	Family
IPR036259	MFS_trans_sf	Homologous_superfamily

Pfam: PF00854

UniProt features (16 total): transmembrane region 11, sequence variant 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NIM6-F1	76.13	0.36

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 41 (showing top): GOBP_TRANSMEMBRANE_TRANSPORT, chr12p12, GOMF_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_SECONDARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_SYMPORTER_ACTIVITY, GOMF_TRANSPORTER_ACTIVITY, PAX3_TARGET_GENES, MIR153_5P, MIR616_5P, MIR371B_5P, MIR373_5P, GSE10094_LCMV_VS_LISTERIA_IND_EFF_CD4_TCELL_DN, MIR144_3P, MIR12123, MIR6885_3P

GO Biological Process (3): protein transport (GO:0015031), peptide transport (GO:0015833), transmembrane transport (GO:0055085)

GO Molecular Function (3): symporter activity (GO:0015293), transmembrane transporter activity (GO:0022857), protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	3
intracellular protein localization	1
establishment of protein localization	1
cellular process	1
secondary active transmembrane transporter activity	1
transporter activity	1
transmembrane transport	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

854 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC15A5	SLC13A5	Q86YT5	953
SLC15A5	SLC13A3	Q8WWT9	734
SLC15A5	SLC13A2	Q13183	730
SLC15A5	KLHL36	Q8N4N3	571
SLC15A5	B3KSW5	B3KSW5	506
SLC15A5	PLEKHA5	Q9HAU0	455
SLC15A5	DCLK2	Q8N568	422
SLC15A5	DCDC2B	A2VCK2	414
SLC15A5	DERA	Q9Y315	408
SLC15A5	ACCSL	Q4AC99	400
SLC15A5	MGST1	P10620	385
SLC15A5	SLC25A35	Q3KQZ1	374
SLC15A5	TMEM267	Q0VDI3	371
SLC15A5	MFSD6L	Q8IWD5	370
SLC15A5	WDR38	Q5JTN6	363

IntAct

263 interactions, top by confidence:

A	B	Type	Score
SLC15A5	SCRIB	psi-mi:“MI:0915”(physical association)	0.780
SCRIB	SLC15A5	psi-mi:“MI:0407”(direct interaction)	0.780
SLC15A5	SCRIB	psi-mi:“MI:0407”(direct interaction)	0.780
PDZK1	SLC15A5	psi-mi:“MI:0407”(direct interaction)	0.620
SLC15A5	PDZK1	psi-mi:“MI:0407”(direct interaction)	0.620
SLC15A5	MAGI2	psi-mi:“MI:0407”(direct interaction)	0.610
MAGI2	SLC15A5	psi-mi:“MI:0915”(physical association)	0.610
PDZRN4	SLC15A5	psi-mi:“MI:0407”(direct interaction)	0.610
PDZRN4	SLC15A5	psi-mi:“MI:0915”(physical association)	0.610
SLC15A5	MAST2	psi-mi:“MI:0407”(direct interaction)	0.610
MAST2	SLC15A5	psi-mi:“MI:0915”(physical association)	0.610
MAGI2	SLC15A5	psi-mi:“MI:0407”(direct interaction)	0.610
SLC15A5	PDZRN4	psi-mi:“MI:0407”(direct interaction)	0.610
SLC15A5	SHANK3	psi-mi:“MI:0407”(direct interaction)	0.440
SLC15A5	MPDZ	psi-mi:“MI:0407”(direct interaction)	0.440
SNX27	SLC15A5	psi-mi:“MI:0407”(direct interaction)	0.440
SLC15A5	SHANK2	psi-mi:“MI:0407”(direct interaction)	0.440
SLC15A5	PDZRN3	psi-mi:“MI:0407”(direct interaction)	0.440

ESM2 similar proteins: A1Z7R6, A6NIM6, A6QNW6, A9JTG4, A9X4U2, E1BPQ3, F4I9E1, F4KIL8, F5H094, G3V0H7, O35913, O80436, O94911, Q497L8, Q497L9, Q4G0N8, Q4R445, Q5BIZ0, Q5BK75, Q5TAH2, Q5XGZ9, Q68EU6, Q6DBX0, Q6TAC4, Q6UJY2, Q7SXB7, Q86UG4, Q8C0X7, Q8CBB2, Q8IUA7, Q8K440, Q8K441, Q8K442, Q8K449, Q8N139, Q8R0C3, Q8R0S9, Q8WWZ4, Q924V4, Q96RN1

Diamond homologs: A6NIM6, Q8CBB2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 110 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Ras activation upon Ca2+ influx through NMDA receptor	5	40.8×	6e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	38.8×	6e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	38.8×	6e-06
Assembly and cell surface presentation of NMDA receptors	10	36.2×	1e-11
Dopamine Neurotransmitter Release Cycle	5	35.5×	8e-06
Long-term potentiation	5	34.0×	9e-06
Neurexins and neuroligins	12	33.8×	2e-13
Protein-protein interactions at synapses	8	30.4×	1e-08

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	12	67.7×	4e-17
protein localization to synapse	7	52.1×	9e-09
receptor clustering	8	48.5×	9e-10
regulation of postsynaptic membrane neurotransmitter receptor levels	7	33.7×	2e-07
social behavior	5	13.2×	1e-03
Rho protein signal transduction	5	12.0×	1e-03
protein-containing complex assembly	10	11.1×	3e-06
cell-cell adhesion	10	9.9×	6e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	89
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1624 predictions. Top by Δscore:

Variant	Effect	Δscore
12:16189812:ATATC:A	acceptor_loss	0.9900
12:16189813:TAT:T	acceptor_gain	0.9900
12:16189814:ATCTA:A	acceptor_loss	0.9900
12:16189815:TCT:T	acceptor_loss	0.9900
12:16189816:C:CC	acceptor_gain	0.9900
12:16189816:CT:C	acceptor_loss	0.9900
12:16224413:CGGG:C	donor_gain	0.9900
12:16224456:A:AC	donor_gain	0.9900
12:16224457:C:CC	donor_gain	0.9900
12:16224505:T:A	donor_gain	0.9900
12:16224603:C:CC	acceptor_gain	0.9900
12:16239672:TGTAC:T	donor_loss	0.9900
12:16239673:GTAC:G	donor_loss	0.9900
12:16239674:TACT:T	donor_loss	0.9900
12:16239675:ACT:A	donor_loss	0.9900
12:16239676:CTTAC:C	donor_loss	0.9900
12:16239677:TTA:T	donor_loss	0.9900
12:16239678:TACT:T	donor_loss	0.9900
12:16239679:A:AC	donor_gain	0.9900
12:16239679:ACTGA:A	donor_loss	0.9900
12:16239680:C:CT	donor_gain	0.9900
12:16239680:CTG:C	donor_gain	0.9900
12:16239866:ATC:A	acceptor_loss	0.9900
12:16239867:TCTG:T	acceptor_loss	0.9900
12:16239868:C:CC	acceptor_gain	0.9900
12:16239868:C:T	acceptor_loss	0.9900
12:16239869:T:C	acceptor_loss	0.9900
12:16272553:CTACT:C	donor_loss	0.9900
12:16272554:TACTT:T	donor_loss	0.9900
12:16272555:ACTTA:A	donor_loss	0.9900

AlphaMissense

3779 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:16224542:C:G	R408P	0.936
12:16194443:A:C	F498L	0.837
12:16194443:A:T	F498L	0.837
12:16194445:A:G	F498L	0.837
12:16224560:C:T	G402D	0.836
12:16194374:G:C	N521K	0.802
12:16194374:G:T	N521K	0.802
12:16239844:T:A	Q333H	0.796
12:16239844:T:G	Q333H	0.796
12:16224550:T:A	E405D	0.793
12:16224550:T:G	E405D	0.793
12:16224551:T:A	E405V	0.792
12:16224561:C:G	G402R	0.787
12:16277485:A:C	F67L	0.787
12:16277485:A:T	F67L	0.787
12:16277487:A:G	F67L	0.787
12:16277428:A:C	F86L	0.784
12:16277428:A:T	F86L	0.784
12:16277430:A:G	F86L	0.784
12:16194448:A:G	W497R	0.774
12:16194448:A:T	W497R	0.774
12:16194393:G:T	A515E	0.763
12:16257831:A:C	F208L	0.758
12:16257831:A:T	F208L	0.758
12:16257833:A:G	F208L	0.758
12:16224563:G:T	A401D	0.746
12:16194444:A:G	F498S	0.740
12:16224597:C:G	G390R	0.740
12:16224597:C:T	G390R	0.740
12:16194362:G:C	F525L	0.738

dbSNP variants (sampled 300 via entrez): RS1000005312 (12:16199491 T>C), RS1000006850 (12:16259346 C>A,G,T), RS1000008817 (12:16218353 T>A), RS1000047058 (12:16237224 G>A,C), RS1000101822 (12:16252972 C>G), RS1000108359 (12:16276007 A>G), RS1000161243 (12:16204907 T>G), RS1000177352 (12:16245615 G>T), RS1000233276 (12:16212587 T>C), RS1000237459 (12:16253245 A>G), RS1000251388 (12:16251613 T>C), RS1000289362 (12:16224435 C>A), RS1000296204 (12:16206427 C>G,T), RS1000364927 (12:16241652 A>G), RS1000408803 (12:16269421 C>G)

Disease associations

OMIM: gene MIM:620324 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST007326_76	Number of sexual partners	4.000000e-08
GCST007576_214	Chronotype	3.000000e-08
GCST007940_1	Medication use (antidepressants)	5.000000e-09
GCST010988_487	Adult body size	3.000000e-08
GCST90026416_16	Mild age-related type 2 diabetes	8.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008328	chronotype measurement
EFO:0009940	Antidepressant use measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
Benzo(a)pyrene	affects methylation	1
Chlordecone	affects response to substance	1

Clinical trials (associated diseases)

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