SLCO6A1

Summary

SLCO6A1 (solute carrier organic anion transporter family member 6A1, HGNC:23613) is a protein-coding gene on chromosome 5q21.1, encoding Solute carrier organic anion transporter family member 6A1 (Q86UG4).

Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Predicted to be located in plasma membrane. Predicted to be part of CatSper complex. Predicted to be active in basolateral plasma membrane.

Source: NCBI Gene 133482 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 104 total
• MANE Select transcript: NM_173488

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23613
Approved symbol	SLCO6A1
Name	solute carrier organic anion transporter family member 6A1
Location	5q21.1
Locus type	gene with protein product
Status	Approved
Aliases	OATP6A1, OATPY, MGC26949, CT48
Ensembl gene	ENSG00000205359
Ensembl biotype	protein_coding
OMIM	613365
Entrez	133482

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000379807, ENST00000389019, ENST00000505407, ENST00000505739, ENST00000506729, ENST00000511588, ENST00000513675, ENST00000514551, ENST00000514765

RefSeq mRNA: 4 — MANE Select: NM_173488 NM_001289002, NM_001289004, NM_001308014, NM_173488

CCDS: CCDS34206, CCDS75282, CCDS78042

Canonical transcript exons

ENST00000506729 — 14 exons

Exon	Start	End
ENSE00001482573	102419826	102420021
ENSE00001482590	102390981	102391045
ENSE00001482592	102399555	102399742
ENSE00001482593	102412990	102413143
ENSE00001504686	102477676	102477861
ENSE00002086117	102371774	102372123
ENSE00003487260	102388688	102388825
ENSE00003527971	102373337	102373494
ENSE00003533944	102475697	102475793
ENSE00003589816	102480177	102480434
ENSE00003623770	102458382	102458491
ENSE00003650672	102459656	102459777
ENSE00003668841	102438617	102438761
ENSE00003894307	102498487	102499001

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 94.79.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0667 / max 64.0541, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62785	0.0439	3
62786	0.0228	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.79	gold quality
left testis	UBERON:0004533	90.55	gold quality
right testis	UBERON:0004534	89.93	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.75	gold quality
testis	UBERON:0000473	88.07	gold quality
adult organism	UBERON:0007023	81.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.34	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	60.30	gold quality
nasal cavity epithelium	UBERON:0005384	54.76	gold quality
nasal cavity mucosa	UBERON:0001826	52.11	gold quality
skin of hip	UBERON:0001554	49.15	silver quality
upper leg skin	UBERON:0004262	49.02	gold quality
colonic epithelium	UBERON:0000397	44.74	silver quality
ascending aorta	UBERON:0001496	44.55	gold quality
thoracic aorta	UBERON:0001515	44.47	gold quality
placenta	UBERON:0001987	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
ectocervix	UBERON:0012249	42.62	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
ventricular zone	UBERON:0003053	42.09	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
middle temporal gyrus	UBERON:0002771	41.26	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting SLCO6A1, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-1197	99.70	67.75	1027
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-3147	99.52	66.34	388
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-4705	99.10	69.10	1091
HSA-MIR-4434	99.10	67.01	1984
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-877-3P	99.09	68.10	1637
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-374A-3P	98.87	67.82	1531
HSA-MIR-4477A	98.83	69.75	2952

Literature-anchored findings (GeneRIF, showing 2)

• High OATP6A1 expression is associated with small cell lung cancer. (PMID:25301452)
• No association of gene SLCO6A1 rs6878284 with schizophrenia; rs7734060 could be a risk locus for major depressive disorder in the Han Chinese population (PMID:26861727)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
mus_musculus	Slco6c1	ENSMUSG00000026331
mus_musculus	Slco6d1	ENSMUSG00000026336
rattus_norvegicus	Slco6c1	ENSRNOG00000013792
rattus_norvegicus	Slco6b1	ENSRNOG00000019252
rattus_norvegicus	Slco6d1	ENSRNOG00000031146
caenorhabditis_elegans		WBGENE00013499
caenorhabditis_elegans		WBGENE00018739
caenorhabditis_elegans		WBGENE00019346

Paralogs (10): SLCO1A2 (ENSG00000084453), SLCO4A1 (ENSG00000101187), SLCO1B3 (ENSG00000111700), SLCO1B1 (ENSG00000134538), SLCO2B1 (ENSG00000137491), SLCO5A1 (ENSG00000137571), SLCO1C1 (ENSG00000139155), SLCO4C1 (ENSG00000173930), SLCO2A1 (ENSG00000174640), SLCO3A1 (ENSG00000176463)

Protein

Protein identifiers

Solute carrier organic anion transporter family member 6A1 — Q86UG4 (reviewed: Q86UG4)

Alternative names: Cancer/testis antigen 48, Gonad-specific transporter, Organic anion-transporting polypeptide 6A1, Organic anion-transporting polypeptide I, Solute carrier family 21 member 19

All UniProt accessions (4): A0A140VJU7, C9J020, Q86UG4, H0Y8R6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

Tissue specificity. Strongly expressed in testis. Weakly expressed in spleen, brain, fetal brain and placenta. Detected in lung tumors.

Similarity. Belongs to the organo anion transporter (TC 2.A.60) family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q86UG4-1	1	yes
Q86UG4-2	2
Q86UG4-3	3

RefSeq proteins (4): NP_001275931, NP_001275933, NP_001294943, NP_775759* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002350	Kazal_dom	Domain
IPR004156	OATP	Family
IPR036058	Kazal_dom_sf	Homologous_superfamily
IPR036259	MFS_trans_sf	Homologous_superfamily

Pfam: PF03137, PF07648

UniProt features (45 total): topological domain 13, transmembrane region 12, glycosylation site 4, sequence variant 4, disulfide bond 3, sequence conflict 3, splice variant 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86UG4-F1	76.61	0.47

Functional residue map

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

Disulfide bonds (3): 502–532, 508–528, 517–549

Glycosylation sites (4): 300, 497, 546, 661

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GOBP_SODIUM_INDEPENDENT_ORGANIC_ANION_TRANSPORT, GOBP_ORGANIC_ANION_TRANSPORT, chr5q21, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_PLASMA_MEMBRANE_REGION, GOCC_BASAL_PART_OF_CELL, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, GOMF_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_SECONDARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_TRANSPORTER_ACTIVITY, MIR30B_5P_MIR30C_5P, MIR30D_5P, MIR30E_5P

GO Biological Process (3): sodium-independent organic anion transport (GO:0043252), monoatomic ion transport (GO:0006811), transmembrane transport (GO:0055085)

GO Molecular Function (2): obsolete sodium-independent organic anion transmembrane transporter activity (GO:0015347), protein binding (GO:0005515)

GO Cellular Component (3): basolateral plasma membrane (GO:0016323), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
transmembrane transport	1
cellular process	1
binding	1
basal plasma membrane	1
plasma membrane region	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

6034 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLCO6A1	CDH1	P12830	987
SLCO6A1	RTKN	Q9BST9	986
SLCO6A1	HPGDS	O60760	972
SLCO6A1	CDC42	P21181	961
SLCO6A1	GSTA1	P08263	906
SLCO6A1	AKT1	P31749	894
SLCO6A1	GSTM2	P28161	892
SLCO6A1	GSTM1	P09488	892
SLCO6A1	GSTP1	P09211	880
SLCO6A1	TP53	P04637	879
SLCO6A1	H3C1	P02295	868
SLCO6A1	SRC	P12931	867
SLCO6A1	H3-3A	P06351	865
SLCO6A1	H3C14	Q71DI3	865
SLCO6A1	H3-5	Q6NXT2	865
SLCO6A1	H3-4	Q16695	865

IntAct

7 interactions, top by confidence:

A	B	Type	Score
SLCO6A1	RPL14	psi-mi:“MI:0915”(physical association)	0.400
SLCO6A1	H2AZ1	psi-mi:“MI:0915”(physical association)	0.400
SLCO6A1	H1-2	psi-mi:“MI:0915”(physical association)	0.400
SLCO6A1	CTSH	psi-mi:“MI:0914”(association)	0.350
SLCO5A1	CAND2	psi-mi:“MI:0914”(association)	0.350
SLCO6A1	NOP56	psi-mi:“MI:0914”(association)	0.350

BioGRID (124): LAPTM4B (Affinity Capture-MS), RNASE7 (Affinity Capture-MS), SLC9A1 (Affinity Capture-MS), CTSH (Affinity Capture-MS), HAL (Affinity Capture-MS), CPA4 (Affinity Capture-MS), PTPN1 (Affinity Capture-MS), ASAH1 (Affinity Capture-MS), EDA (Affinity Capture-MS), TTYH3 (Affinity Capture-MS), PSMD11 (Affinity Capture-MS), TGM1 (Affinity Capture-MS), SLCO6A1 (Proximity Label-MS), SLCO6A1 (Proximity Label-MS), SLCO6A1 (Proximity Label-MS)

ESM2 similar proteins: A1A4F0, A2QM49, A2ZIM4, E1BPQ3, E2R4X3, F4IXT6, N4WW42, O49567, O57428, O81514, P0C941, P18380, P38279, P50581, P52885, P56180, P68253, P86214, P86252, P86265, Q01741, Q0C8A7, Q0DWQ7, Q2QWX8, Q2RBJ4, Q2XXR3, Q3SZ89, Q4R6N0, Q5GH77, Q5HYJ1, Q5ZHX6, Q66H96, Q6UXP3, Q6YXZ1, Q7X7E9, Q7XT08, Q866X0, Q86UG4, Q86V35, Q8BFZ1

Diamond homologs: F5H094, G3V0H7, O35913, O88397, O94956, P46721, P70502, Q00910, Q5RFF0, Q6ZQN7, Q71MB6, Q86UG4, Q8BGD4, Q8BXB6, Q8HYW2, Q8K078, Q8R3L5, Q91YY5, Q92959, Q96BD0, Q99J94, Q99N01, Q99N02, Q9EP96, Q9EPT5, Q9ERB5, Q9H2Y9, Q9JHI3, Q9JJL3, Q9NPD5, Q9NYB5, Q9QXZ6, Q9QYE2, Q9QZX8, Q9UIG8, Q9Y6L6, P46720, Q8C0X7, Q9EPZ7, A2ASQ1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	79
Likely benign	13
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

3163 predictions. Top by Δscore:

Variant	Effect	Δscore
5:102405024:T:C	acceptor_gain	1.0000
5:102475695:A:AC	donor_gain	1.0000
5:102475696:C:CC	donor_gain	1.0000
5:102480343:A:C	donor_gain	1.0000
5:102373437:T:TC	acceptor_gain	0.9900
5:102373495:C:CA	acceptor_loss	0.9900
5:102373496:T:C	acceptor_loss	0.9900
5:102399641:ATAG:A	donor_gain	0.9900
5:102405018:A:C	acceptor_gain	0.9900
5:102405024:T:TC	acceptor_gain	0.9900
5:102419907:A:AC	donor_gain	0.9900
5:102421817:T:TA	donor_gain	0.9900
5:102458398:AAAT:A	donor_gain	0.9900
5:102475696:CT:C	donor_gain	0.9900
5:102475696:CTTTG:C	donor_gain	0.9900
5:102480281:A:AC	donor_gain	0.9900
5:102480282:C:CC	donor_gain	0.9900
5:102480432:CAC:C	acceptor_gain	0.9900
5:102480433:ACCTA:A	acceptor_loss	0.9900
5:102480435:C:CA	acceptor_loss	0.9900
5:102480440:A:AC	acceptor_gain	0.9900
5:102480442:G:C	acceptor_gain	0.9900
5:102373443:A:C	acceptor_gain	0.9800
5:102373495:C:CC	acceptor_gain	0.9800
5:102388064:A:C	donor_gain	0.9800
5:102388686:A:AC	donor_gain	0.9800
5:102388687:C:CC	donor_gain	0.9800
5:102399637:A:C	donor_gain	0.9800
5:102399740:CAT:C	acceptor_gain	0.9800
5:102412989:C:CG	donor_loss	0.9800

AlphaMissense

4681 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:102413021:C:G	C532S	0.993
5:102413022:A:T	C532S	0.993
5:102399728:A:C	C547W	0.990
5:102399729:C:G	C547S	0.988
5:102399730:A:T	C547S	0.988
5:102413022:A:G	C532R	0.988
5:102413020:A:C	C532W	0.987
5:102413040:A:G	S526P	0.986
5:102413066:C:G	C517S	0.985
5:102413067:A:T	C517S	0.985
5:102413093:C:G	C508S	0.985
5:102413094:A:T	C508S	0.985
5:102399729:C:T	C547Y	0.984
5:102413027:G:T	A530E	0.984
5:102413032:G:C	C528W	0.984
5:102413111:C:G	C502S	0.984
5:102413112:A:T	C502S	0.984
5:102399723:C:G	C549S	0.983
5:102399724:A:T	C549S	0.983
5:102399730:A:G	C547R	0.983
5:102413025:C:A	G531W	0.983
5:102413033:C:G	C528S	0.983
5:102413034:A:T	C528S	0.983
5:102399657:C:G	C571S	0.982
5:102399658:A:T	C571S	0.982
5:102399723:C:T	C549Y	0.982
5:102413021:C:T	C532Y	0.982
5:102413046:A:C	Y524D	0.981
5:102399724:A:G	C549R	0.979
5:102413034:A:G	C528R	0.979

dbSNP variants (sampled 300 via entrez): RS1000001316 (5:102453221 T>G), RS1000011545 (5:102463220 A>G), RS1000056480 (5:102464049 G>A), RS1000064510 (5:102457216 G>A,C), RS1000112054 (5:102415811 A>T), RS1000113524 (5:102414534 A>G), RS1000119065 (5:102477967 T>C), RS1000124243 (5:102378247 G>T), RS1000128708 (5:102455736 T>C), RS1000135724 (5:102426665 T>C), RS1000144605 (5:102414268 T>A), RS1000179812 (5:102417137 A>G), RS1000224679 (5:102377374 A>C), RS1000243552 (5:102408043 T>C,G), RS1000257853 (5:102378208 A>G)

Disease associations

OMIM: gene MIM:613365 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST000435_4	Schizophrenia	1.000000e-06
GCST001438_5	Crohn’s disease	2.000000e-08
GCST002149_13	Schizophrenia	9.000000e-09
GCST002320_3	Cognitive decline (age-related)	7.000000e-07
GCST009379_41	Type 2 diabetes	5.000000e-09
GCST90020027_891	Waist-hip index	4.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs12658397	SLCO6A1		0.00	0

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — SLCO family of organic anion transporting polypeptides

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, increases expression	3
Vorinostat	affects cotreatment, increases expression	2
sodium arsenite	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
3-iodothyronamine	affects uptake	1
dorsomorphin	affects cotreatment, increases expression	1
Benzo(a)pyrene	increases methylation	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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