SLC44A3

Summary

SLC44A3 (solute carrier family 44 member 3, HGNC:28689) is a protein-coding gene on chromosome 1p21.3, encoding Choline transporter-like protein 3 (Q8N4M1).

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

Source: NCBI Gene 126969 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 106 total
• MANE Select transcript: NM_001114106

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28689
Approved symbol	SLC44A3
Name	solute carrier family 44 member 3
Location	1p21.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC45474, CTL3
Ensembl gene	ENSG00000143036
Ensembl biotype	protein_coding
OMIM	620328
Entrez	126969

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 19 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000271227, ENST00000422520, ENST00000446120, ENST00000467909, ENST00000475883, ENST00000527077, ENST00000529450, ENST00000530397, ENST00000532427, ENST00000532670, ENST00000879625, ENST00000879626, ENST00000879627, ENST00000879628, ENST00000879629, ENST00000879630, ENST00000879631, ENST00000958850, ENST00000958851, ENST00000958852, ENST00000958853

RefSeq mRNA: 8 — MANE Select: NM_001114106 NM_001114106, NM_001258340, NM_001258341, NM_001258342, NM_001258343, NM_001301079, NM_001350223, NM_152369

CCDS: CCDS44176, CCDS58011, CCDS58012, CCDS58013, CCDS72827, CCDS751

Canonical transcript exons

ENST00000271227 — 15 exons

Exon	Start	End
ENSE00001847709	94820357	94820478
ENSE00001866133	94894818	94895246
ENSE00003480500	94820949	94821056
ENSE00003511807	94867331	94867417
ENSE00003512522	94837711	94837871
ENSE00003513068	94839948	94840037
ENSE00003518393	94845278	94845464
ENSE00003550492	94827507	94827643
ENSE00003571107	94842000	94842124
ENSE00003571734	94828493	94828586
ENSE00003589704	94824493	94824635
ENSE00003595408	94864743	94864899
ENSE00003609773	94892281	94892517
ENSE00003634298	94891130	94891267
ENSE00003668256	94857335	94857500

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 94.42.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4581 / max 64.0709, expressed in 553 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4105	1.3526	540
4106	0.1055	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	94.42	gold quality
rectum	UBERON:0001052	92.88	gold quality
ileal mucosa	UBERON:0000331	92.55	gold quality
body of pancreas	UBERON:0001150	92.28	gold quality
lower esophagus mucosa	UBERON:0035834	91.58	gold quality
colonic mucosa	UBERON:0000317	90.86	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.43	gold quality
pancreas	UBERON:0001264	90.42	gold quality
palpebral conjunctiva	UBERON:0001812	89.89	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.58	gold quality
adult mammalian kidney	UBERON:0000082	89.51	gold quality
kidney epithelium	UBERON:0004819	89.38	gold quality
metanephros cortex	UBERON:0010533	89.14	gold quality
islet of Langerhans	UBERON:0000006	88.94	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.64	gold quality
kidney	UBERON:0002113	87.97	gold quality
transverse colon	UBERON:0001157	87.89	gold quality
duodenum	UBERON:0002114	87.58	gold quality
eye	UBERON:0000970	87.39	gold quality
metanephros	UBERON:0000081	87.09	gold quality
minor salivary gland	UBERON:0001830	86.86	gold quality
pituitary gland	UBERON:0000007	86.58	gold quality
adenohypophysis	UBERON:0002196	86.03	gold quality
jejunal mucosa	UBERON:0000399	85.60	gold quality
body of stomach	UBERON:0001161	85.51	gold quality
right uterine tube	UBERON:0001302	85.36	gold quality
saliva-secreting gland	UBERON:0001044	84.92	gold quality
cortex of kidney	UBERON:0001225	84.87	gold quality
epithelial cell of pancreas	CL:0000083	84.61	gold quality
stomach	UBERON:0000945	84.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting SLC44A3, 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-1252-5P	100.00	69.80	2774
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-548AI	99.69	69.24	1494
HSA-MIR-548BA	99.69	69.14	1514
HSA-MIR-570-5P	99.69	69.24	1494
HSA-MIR-26A-1-3P	99.64	66.81	788
HSA-MIR-26A-2-3P	99.64	66.82	786
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-629-5P	98.78	68.72	1032
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-4277	98.34	67.17	1323
HSA-MIR-4778-5P	97.96	68.06	1634
HSA-MIR-3129-3P	97.85	67.63	1246
HSA-MIR-5583-5P	97.85	67.61	1243
HSA-MIR-8057	97.64	66.54	897

Literature-anchored findings (GeneRIF, showing 1)

• Genome-Wide Analysis of Exertional Rhabdomyolysis in Sickle Cell Trait Positive African Americans. (PMID:38674343)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc44a1a	ENSDARG00000015946
mus_musculus	Slc44a3	ENSMUSG00000039865
rattus_norvegicus	Slc44a3	ENSRNOG00000011723
drosophila_melanogaster	Ctl1	FBGN0035523
drosophila_melanogaster	Ctl2	FBGN0039637
caenorhabditis_elegans		WBGENE00018037

Paralogs (4): SLC44A1 (ENSG00000070214), SLC44A2 (ENSG00000129353), SLC44A5 (ENSG00000137968), SLC44A4 (ENSG00000204385)

Protein

Protein identifiers

Choline transporter-like protein 3 — Q8N4M1 (reviewed: Q8N4M1)

Alternative names: Solute carrier family 44 member 3

All UniProt accessions (5): Q8N4M1, E9PIC5, F8W7F3, H0YD35, H0YDW5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the CTL (choline transporter-like) family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q8N4M1-1	1	yes
Q8N4M1-2	2
Q8N4M1-3	3
Q8N4M1-4	4
Q8N4M1-5	5
Q8N4M1-6	6

RefSeq proteins (8): NP_001107578, NP_001245269, NP_001245270, NP_001245271, NP_001245272, NP_001288008, NP_001337152, NP_689582 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007603	Choline_transptr-like	Family

Pfam: PF04515

UniProt features (24 total): transmembrane region 8, glycosylation site 5, splice variant 4, sequence variant 2, sequence conflict 2, chain 1, compositionally biased region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4M1-F1	81.32	0.33

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): 136, 151, 412, 503, 521

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-1483191	Synthesis of PC
R-HSA-9958517	SLC-mediated bile acid transport
R-HSA-425366

MSigDB gene sets: 77 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_BIOSYNTHETIC_PROCESS, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, HNF1_Q6, CHX10_01, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, NKX62_Q2, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, LIAO_METASTASIS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS

GO Biological Process (3): phosphatidylcholine biosynthetic process (GO:0006656), transmembrane transport (GO:0055085), choline transport (GO:0015871)

GO Molecular Function (3): choline transmembrane transporter activity (GO:0015220), transmembrane transporter activity (GO:0022857), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1
SLC-mediated transport of organic anions	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phosphatidylcholine metabolic process	1
glycerophospholipid biosynthetic process	1
transport	1
cellular process	1
nitrogen compound transport	1
choline transport	1
transmembrane transporter activity	1
transporter activity	1
transmembrane transport	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

852 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC44A3	ZNF428	Q96B54	656
SLC44A3	MAS1	P04201	642
SLC44A3	CIAPIN1	Q6FI81	617
SLC44A3	UBL7	Q96S82	534
SLC44A3	SLC5A7	Q9GZV3	520
SLC44A3	RNF208	Q9H0X6	506
SLC44A3	SLC36A2	Q495M3	489
SLC44A3	STPG1	Q5TH74	478
SLC44A3	SLC13A2	Q13183	412
SLC44A3	EGFR	P00533	398
SLC44A3	ASAH1	Q13510	373
SLC44A3	HMCES	Q96FZ2	370
SLC44A3	SLC22A16	Q86VW1	366
SLC44A3	SLC46A2	Q9BY10	360
SLC44A3	POMGNT2	Q8NAT1	355

IntAct

6 interactions, top by confidence:

A	B	Type	Score
FHL3	SLC44A3	psi-mi:“MI:0915”(physical association)	0.560
SLC44A3	FHL3	psi-mi:“MI:0915”(physical association)	0.560
SLC44A3	RNF181	psi-mi:“MI:0915”(physical association)	0.400
SLC44A3	CLGN	psi-mi:“MI:0914”(association)	0.350

BioGRID (63): SLC44A3 (Two-hybrid), SLC44A3 (Two-hybrid), SLC44A3 (Two-hybrid), RNF181 (Affinity Capture-MS), AMFR (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ATP13A1 (Affinity Capture-MS), BAG5 (Affinity Capture-MS), CADM1 (Affinity Capture-MS), CLGN (Affinity Capture-MS), CNTNAP2 (Affinity Capture-MS), CYP51A1 (Affinity Capture-MS), DEGS1 (Affinity Capture-MS), DLG1 (Affinity Capture-MS), DNAJC16 (Affinity Capture-MS)

ESM2 similar proteins: A1A5B4, A2AHL1, A2BIE7, A2RRU4, A5PK40, A6NDV4, A6QLK4, A6QM06, B1AWJ5, E9PTA2, E9Q6C8, O94759, P86044, P97260, Q04671, Q12770, Q17QL9, Q3TD49, Q49LS8, Q4R7X9, Q5F383, Q5GH57, Q5MNU5, Q5PQL3, Q5RBY7, Q5ZMP3, Q60HE8, Q6AY05, Q6GQT6, Q6UX01, Q7RTT9, Q7TN60, Q7Z403, Q8IU68, Q8MIQ9, Q8N4M1, Q8R139, Q8R4F0, Q8TCT7, Q91YD4

Diamond homologs: A5PK40, Q17JQ7, Q6AY92, Q6GN42, Q6IP59, Q6IR74, Q6X893, Q7PRJ0, Q7Q5R7, Q7SYC9, Q810F1, Q8N4M1, Q8VII6, Q8WWI5, Q921V7, Q9I9B9, Q9VAP3, Q9VZE7, A3KMY4, A5D7H3, A5PF08, A5PMW0, A8XKF2, B0JZD0, B0S5A7, B4F795, B5X3W7, F1S584, Q20026, Q4I8E9, Q53GD3, Q5R5L9, Q5RJI2, Q6C938, Q6MG71, Q7T2B0, Q869R1, Q8BY89, Q8IWA5, Q8NCS7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2624 predictions. Top by Δscore:

Variant	Effect	Δscore
1:94824487:TGCCA:T	acceptor_loss	1.0000
1:94824488:GCCA:G	acceptor_loss	1.0000
1:94824489:CCAGG:C	acceptor_loss	1.0000
1:94824490:CAGG:C	acceptor_loss	1.0000
1:94824492:GGT:G	acceptor_gain	1.0000
1:94824631:AAAAA:A	donor_gain	1.0000
1:94824632:AAAA:A	donor_gain	1.0000
1:94824632:AAAAG:A	donor_loss	1.0000
1:94824633:AAA:A	donor_gain	1.0000
1:94824634:AA:A	donor_gain	1.0000
1:94824635:AGTA:A	donor_loss	1.0000
1:94824636:G:C	donor_loss	1.0000
1:94824636:G:GG	donor_gain	1.0000
1:94824637:TAAG:T	donor_loss	1.0000
1:94827495:T:G	acceptor_gain	1.0000
1:94827505:A:AG	acceptor_gain	1.0000
1:94827506:G:GA	acceptor_gain	1.0000
1:94827506:GA:G	acceptor_gain	1.0000
1:94827506:GAC:G	acceptor_gain	1.0000
1:94827506:GACAC:G	acceptor_gain	1.0000
1:94827641:GTG:G	donor_gain	1.0000
1:94864741:A:AG	acceptor_gain	1.0000
1:94864742:G:GG	acceptor_gain	1.0000
1:94864742:GAA:G	acceptor_gain	1.0000
1:94867319:AACCT:A	acceptor_gain	1.0000
1:94867323:T:TA	acceptor_gain	1.0000
1:94891129:GA:G	acceptor_gain	1.0000
1:94891264:A:T	donor_gain	1.0000
1:94891264:AAAG:A	donor_loss	1.0000
1:94891265:AAGG:A	donor_loss	1.0000

AlphaMissense

4294 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:94824571:T:A	C72S	0.989
1:94824572:G:C	C72S	0.989
1:94837736:T:A	C179S	0.987
1:94837737:G:C	C179S	0.987
1:94827574:T:A	C116S	0.984
1:94827575:G:C	C116S	0.984
1:94828561:T:A	C162S	0.979
1:94828562:G:C	C162S	0.979
1:94827586:T:A	C120S	0.978
1:94827587:G:C	C120S	0.978
1:94837736:T:C	C179R	0.978
1:94828504:T:A	C143S	0.976
1:94828505:G:C	C143S	0.976
1:94828577:T:A	V167D	0.973
1:94827574:T:C	C116R	0.969
1:94827575:G:A	C116Y	0.968
1:94828504:T:C	C143R	0.968
1:94842017:T:A	W260R	0.968
1:94842017:T:C	W260R	0.968
1:94827576:T:G	C116W	0.967
1:94837737:G:A	C179Y	0.966
1:94824563:G:T	G69V	0.965
1:94824554:A:T	D66V	0.964
1:94827586:T:C	C120R	0.964
1:94824553:G:C	D66H	0.963
1:94824571:T:C	C72R	0.963
1:94837738:T:G	C179W	0.963
1:94824567:C:A	N70K	0.962
1:94824567:C:G	N70K	0.962
1:94824555:C:A	D66E	0.960

dbSNP variants (sampled 300 via entrez): RS1000000264 (1:94873859 A>T), RS1000039889 (1:94849135 T>A,C), RS1000091701 (1:94833923 G>A), RS1000128873 (1:94886085 C>A,T), RS1000145508 (1:94888286 T>A), RS1000180278 (1:94883268 A>G), RS1000232494 (1:94883596 T>C), RS1000412932 (1:94821515 A>T), RS1000422993 (1:94861058 A>G), RS1000429968 (1:94889537 C>T), RS1000456504 (1:94874110 T>A), RS1000510443 (1:94840337 T>C), RS1000582989 (1:94884975 G>A), RS1000599198 (1:94845013 T>C), RS1000639965 (1:94879188 G>C)

Disease associations

OMIM: gene MIM:620328 | 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
GCST001369_1	Type 2 diabetes	6.000000e-06
GCST002120_18	Metabolite levels (Dihydroxy docosatrienoic acid)	4.000000e-06
GCST011365_90	Myocardial infarction	1.000000e-08
GCST011826_1	Computer vision syndrome	2.000000e-06
GCST90014033_2	Haemorrhoidal disease	6.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005275	dihydroxy docosatrienoic acid measurement

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
rs3818929	SLC44A3		0.00	0

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — SLC44 choline transporter-like family

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects cotreatment, increases expression	6
Cyclosporine	decreases expression	4
mercuric bromide	affects cotreatment, increases expression	2
entinostat	increases expression, affects cotreatment	2
(+)-JQ1 compound	decreases expression	2
Air Pollutants	increases abundance, decreases expression	2
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	2
Estradiol	affects cotreatment, increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tetrachlorodibenzodioxin	increases expression	2
Tretinoin	decreases expression, increases expression	2
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
alpha phellandrene	increases expression	1
bisphenol A	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, 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
belinostat	decreases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
NSC 689534	increases expression	1
Acetaminophen	decreases expression	1
Azathioprine	decreases expression	1
Diethylhexyl Phthalate	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Progesterone	affects cotreatment, increases expression	1
Quercetin	decreases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4P8	HCT116-SLC44A3-KO-c2	Cancer cell line	Male
CVCL_D4P9	HCT116-SLC44A3-KO-c8	Cancer cell line	Male
CVCL_TN78	HAP1 SLC44A3 (-) 1	Cancer cell line	Male
CVCL_XT31	HAP1 SLC44A3 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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