SLC10A3

Summary

SLC10A3 (solute carrier family 10 member 3, HGNC:22979) is a protein-coding gene on chromosome Xq28, encoding P3 protein (P09131). The ubiquitous expression and the conservation of the sequence in distant animal species suggest that the gene codes for a protein with housekeeping functions.

This gene maps to a GC-rich region of the X chromosome and was identified by its proximity to a CpG island. It is thought to be a housekeeping gene. Alternative splicing results in multiple transcript variants encoding distinct isoforms.

Source: NCBI Gene 8273 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 73 total
• MANE Select transcript: NM_019848

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22979
Approved symbol	SLC10A3
Name	solute carrier family 10 member 3
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	P3, DXS253E
Ensembl gene	ENSG00000126903
Ensembl biotype	protein_coding
OMIM	312090
Entrez	8273

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 15 protein_coding

ENST00000263512, ENST00000369649, ENST00000393586, ENST00000393587, ENST00000453912, ENST00000651600, ENST00000882890, ENST00000882891, ENST00000882892, ENST00000882893, ENST00000882894, ENST00000882895, ENST00000922672, ENST00000922673, ENST00000922674

RefSeq mRNA: 3 — MANE Select: NM_019848 NM_001142391, NM_001142392, NM_019848

CCDS: CCDS14755, CCDS48195

Canonical transcript exons

ENST00000651600 — 2 exons

Exon	Start	End
ENSE00003841872	154490307	154490629
ENSE00003843615	154487311	154489082

Expression profiles

Bgee: expression breadth ubiquitous, 229 present calls, max score 91.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.4910 / max 267.7466, expressed in 1813 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
201036	30.7797	1806
201037	8.7113	1772

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right coronary artery	UBERON:0001625	91.44	gold quality
descending thoracic aorta	UBERON:0002345	91.41	gold quality
skin of leg	UBERON:0001511	91.38	gold quality
thoracic aorta	UBERON:0001515	91.30	gold quality
ascending aorta	UBERON:0001496	91.25	gold quality
stromal cell of endometrium	CL:0002255	91.13	gold quality
right ovary	UBERON:0002118	91.04	gold quality
lower esophagus mucosa	UBERON:0035834	90.60	gold quality
aorta	UBERON:0000947	90.52	gold quality
granulocyte	CL:0000094	90.42	gold quality
decidua	UBERON:0002450	90.29	gold quality
skin of abdomen	UBERON:0001416	90.27	gold quality
left ovary	UBERON:0002119	90.25	gold quality
popliteal artery	UBERON:0002250	90.09	gold quality
tibial artery	UBERON:0007610	90.08	gold quality
left coronary artery	UBERON:0001626	89.78	gold quality
left uterine tube	UBERON:0001303	89.77	gold quality
gingival epithelium	UBERON:0001949	89.70	gold quality
apex of heart	UBERON:0002098	89.36	gold quality
zone of skin	UBERON:0000014	89.28	gold quality
coronary artery	UBERON:0001621	89.25	gold quality
gingiva	UBERON:0001828	89.13	gold quality
mucosa of stomach	UBERON:0001199	89.08	gold quality
ectocervix	UBERON:0012249	89.05	gold quality
esophagus mucosa	UBERON:0002469	88.91	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	88.80	gold quality
gall bladder	UBERON:0002110	88.69	gold quality
body of uterus	UBERON:0009853	88.60	gold quality
esophagus	UBERON:0001043	88.36	gold quality
endocervix	UBERON:0000458	88.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting SLC10A3, 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-6873-3P	100.00	71.42	2626
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-6744-3P	99.22	64.41	972
HSA-MIR-6797-3P	99.17	66.94	668
HSA-MIR-4757-5P	99.12	64.51	981
HSA-MIR-1909-5P	98.94	64.01	484
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-6076	98.61	65.69	637
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-876-5P	97.99	68.49	1345

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc10a3	ENSDARG00000103220
mus_musculus	Slc10a3	ENSMUSG00000032806
rattus_norvegicus	Slc10a3	ENSRNOG00000060580
drosophila_melanogaster	CG11655	FBGN0030638
drosophila_melanogaster	CG9903	FBGN0030756
caenorhabditis_elegans		WBGENE00044650

Paralogs (5): SLC10A1 (ENSG00000100652), SLC10A2 (ENSG00000125255), SLC10A4 (ENSG00000145248), SLC10A6 (ENSG00000145283), SLC10A5 (ENSG00000253598)

Protein

Protein identifiers

P3 protein — P09131 (reviewed: P09131)

Alternative names: Solute carrier family 10 member 3

All UniProt accessions (3): P09131, A0A0A0MS43, Q5HY78

UniProt curated annotations — full annotation on UniProt →

Function. The ubiquitous expression and the conservation of the sequence in distant animal species suggest that the gene codes for a protein with housekeeping functions.

Subcellular location. Membrane.

Similarity. Belongs to the bile acid:sodium symporter (BASS) (TC 2.A.28) family.

Isoforms (2)

UniProt ID	Names	Canonical?
P09131-1	1	yes
P09131-2	2

RefSeq proteins (3): NP_001135863, NP_001135864, NP_062822* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002657	BilAc:Na_symport/Acr3	Family
IPR004710	Bilac:Na_transpt	Family
IPR038770	Na+/solute_symporter_sf	Homologous_superfamily
IPR057103	NTCP5_P3_N	Domain

Pfam: PF01758, PF24690

UniProt features (12 total): transmembrane region 8, chain 1, splice variant 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P09131-F1	77.41	0.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 133 (showing top): CTATGCA_MIR153, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_ORGANIC_ACID_TRANSPORT, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, GOBP_ORGANIC_ANION_TRANSPORT, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_BILE_ACID_AND_BILE_SALT_TRANSPORT, GOBP_RESPONSE_TO_LIPID, GOBP_MONOCARBOXYLIC_ACID_TRANSPORT, GOBP_RESPONSE_TO_RETINOIC_ACID, LIU_CMYB_TARGETS_UP, KIM_WT1_TARGETS_12HR_UP, GOBP_LIPID_LOCALIZATION, MILI_PSEUDOPODIA_CHEMOTAXIS_DN, GOBP_TRANSMEMBRANE_TRANSPORT

GO Biological Process (3): bile acid and bile salt transport (GO:0015721), response to retinoic acid (GO:0032526), transmembrane transport (GO:0055085)

GO Molecular Function (2): bile acid:sodium symporter activity (GO:0008508), symporter activity (GO:0015293)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid transport	1
monocarboxylic acid transport	1
organic hydroxy compound transport	1
response to lipid	1
response to oxygen-containing compound	1
transport	1
cellular process	1
organic acid:sodium symporter activity	1
bile acid transmembrane transporter activity	1
secondary active monocarboxylate transmembrane transporter activity	1
secondary active transmembrane transporter activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

648 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC10A3	SLC12A1	Q13621	776
SLC10A3	SLC10A7	Q0GE19	753
SLC10A3	GOLPH3	Q9H4A6	602
SLC10A3	SLC12A2	P55011	528
SLC10A3	VMA12	Q8N511	477
SLC10A3	SLC12A3	P55017	402
SLC10A3	UBL4A	P11441	369
SLC10A3	RTL5	Q5HYW3	347
SLC10A3	TTC16	Q8NEE8	341
SLC10A3	TEX261	Q6UWH6	338
SLC10A3	OCA2	Q04671	329
SLC10A3	SLC35B3	Q9H1N7	327
SLC10A3	FBN1	P35555	304
SLC10A3	SLC10A2	Q12908	301
SLC10A3	SLC10A1	Q14973	298

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SORBS1	SLC10A3	psi-mi:“MI:0915”(physical association)	0.370
SLC10A3	CPD	psi-mi:“MI:0914”(association)	0.350

BioGRID (22): SLC10A3 (Affinity Capture-RNA), SLC10A3 (Affinity Capture-RNA), SLC10A3 (Affinity Capture-RNA), SLC10A3 (Co-fractionation), SLC10A3 (Co-fractionation), SLC10A3 (Co-fractionation), SLC10A3 (Co-fractionation), SLC10A3 (Co-fractionation), SLC10A3 (Co-fractionation), SLC10A3 (Co-fractionation), TVP23B (Co-fractionation), YIPF1 (Co-fractionation), YIPF2 (Co-fractionation), YIPF6 (Co-fractionation), ACTG1 (Affinity Capture-MS)

ESM2 similar proteins: A0AV02, A2AWR3, A2VCW5, A4QN56, A6QP84, B2RXV4, D4A7H1, F7B113, G8XYX6, O08705, O70324, P09131, P19634, P21129, P23791, P26431, P26434, P26435, P36021, P48761, P48762, P97751, Q0V8N6, Q14973, Q28036, Q3KNW5, Q3UEZ8, Q4JLT5, Q5PT54, Q5PT56, Q5R9A7, Q61165, Q70EX6, Q71RS6, Q7Z3F1, Q8BFW9, Q8BLV3, Q8BUE1, Q8BZ00, Q8C261

Diamond homologs: A6QP84, O08705, P09131, P26435, P70172, Q12908, Q14973, Q28727, Q3KNW5, Q3UEZ8, Q4JLT5, Q5PT55, Q5PT56, Q60414, Q62633, Q70EX6, Q7XVB3, Q96EP9, Q9CXB2, B8BDK4, F4JPW1, O34524, P21129, Q1EBV7, Q5PT54, Q5VRB2, Q650U0, Q6K739, Q8RXE8, Q8VYY4, Q8ZKL0, Q93YR2, Q0V8N6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	41
Likely benign	8
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

501 predictions. Top by Δscore:

Variant	Effect	Δscore
X:154489081:CC:C	acceptor_gain	0.9900
X:154489082:CC:C	acceptor_gain	0.9900
X:154489083:C:CC	acceptor_gain	0.9900
X:154489091:G:GC	acceptor_gain	0.9900
X:154489078:TGTCC:T	acceptor_gain	0.9800
X:154489083:C:CA	acceptor_loss	0.9800
X:154489083:C:T	acceptor_gain	0.9800
X:154489084:T:A	acceptor_loss	0.9800
X:154489091:G:C	acceptor_gain	0.9800
X:154489999:A:T	acceptor_gain	0.9800
X:154489080:TCC:T	acceptor_gain	0.9700
X:154489081:CCC:C	acceptor_gain	0.9700
X:154490301:CCCTA:C	donor_loss	0.9700
X:154490302:CCTA:C	donor_loss	0.9700
X:154490303:CTA:C	donor_loss	0.9700
X:154490304:TA:T	donor_loss	0.9700
X:154490305:A:AT	donor_loss	0.9700
X:154490306:CCT:C	donor_loss	0.9700
X:154488947:T:TA	donor_gain	0.9600
X:154489998:C:CT	acceptor_gain	0.9600
X:154489079:GTCC:G	acceptor_gain	0.9500
X:154490618:G:C	donor_gain	0.9500
X:154489730:G:A	donor_gain	0.9300
X:154490058:C:CT	acceptor_gain	0.9000
X:154490508:C:A	donor_gain	0.9000
X:154489713:CA:C	donor_gain	0.8900
X:154490587:CTCT:C	donor_loss	0.8900
X:154490588:TCTCA:T	donor_loss	0.8900
X:154490589:CTCA:C	donor_loss	0.8900
X:154490590:TCA:T	donor_loss	0.8900

AlphaMissense

3056 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:154487864:G:C	S359R	0.996
X:154487864:G:T	S359R	0.996
X:154487866:T:G	S359R	0.996
X:154488119:G:C	S274R	0.995
X:154488119:G:T	S274R	0.995
X:154488121:T:G	S274R	0.995
X:154487687:G:C	S418R	0.994
X:154487687:G:T	S418R	0.994
X:154487689:T:G	S418R	0.994
X:154487943:G:C	P333R	0.994
X:154487663:G:C	S426R	0.993
X:154487663:G:T	S426R	0.993
X:154487665:T:G	S426R	0.993
X:154487666:G:C	N425K	0.993
X:154487666:G:T	N425K	0.993
X:154487691:A:T	V417D	0.993
X:154488168:A:G	L258P	0.993
X:154488172:C:G	G257R	0.993
X:154488318:C:T	G208E	0.993
X:154488328:A:G	C205R	0.993
X:154487943:G:T	P333H	0.992
X:154488171:C:T	G257D	0.991
X:154487605:A:G	S446P	0.988
X:154487931:C:T	G337D	0.988
X:154488707:A:C	F78L	0.988
X:154488707:A:T	F78L	0.988
X:154488709:A:G	F78L	0.988
X:154488157:A:G	C262R	0.986
X:154488708:A:C	F78C	0.986
X:154488057:G:T	A295D	0.985

dbSNP variants (sampled 300 via entrez): RS1000882856 (X:154487666 G>A), RS1001532201 (X:154492412 G>A,T), RS1001759527 (X:154491944 C>T), RS1003194654 (X:154490729 C>T), RS1003245410 (X:154491006 C>T), RS1003433708 (X:154490433 G>A,C), RS1004059292 (X:154490741 C>A), RS1004514309 (X:154491054 T>C), RS1005779722 (X:154489346 G>A), RS1008236188 (X:154491571 T>G), RS1010576976 (X:154490327 G>A), RS1011999814 (X:154491875 C>A,T), RS1015067015 (X:154492503 G>A), RS1016838133 (X:154491068 G>C), RS1017141046 (X:154490748 G>A,C)

Disease associations

OMIM: gene MIM:312090 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

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 — SLC10 family of sodium-bile acid co-transporters

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	2
aristolochic acid I	increases expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	decreases expression	1
cupric chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
ICG 001	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Estradiol	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Triclosan	increases expression	1
Urethane	increases expression	1
Valproic Acid	affects expression	1
Zidovudine	increases expression	1
Aflatoxin B1	affects expression	1
Okadaic Acid	increases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4HF	HCT116-SLC10A3-KO-c2	Cancer cell line	Male
CVCL_D4HG	HCT116-SLC10A3-KO-c6	Cancer cell line	Male
CVCL_TL41	HAP1 SLC10A3 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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