SLC44A5

Summary

SLC44A5 (solute carrier family 44 member 5, HGNC:28524) is a protein-coding gene on chromosome 1p31.1, encoding Choline transporter-like protein 5 (Q8NCS7). Choline/H+ antiporter.

Enables choline transmembrane transporter activity. Involved in choline transport. Located in plasma membrane.

Source: NCBI Gene 204962 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 94 total
• MANE Select transcript: NM_001130058

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28524
Approved symbol	SLC44A5
Name	solute carrier family 44 member 5
Location	1p31.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC34032, CTL5
Ensembl gene	ENSG00000137968
Ensembl biotype	protein_coding
OMIM	620329
Entrez	204962

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000370855, ENST00000370859, ENST00000469525

RefSeq mRNA: 6 — MANE Select: NM_001130058 NM_001130058, NM_001320283, NM_001320285, NM_001320287, NM_001394064, NM_152697

CCDS: CCDS44164, CCDS667

Canonical transcript exons

ENST00000370859 — 24 exons

Exon	Start	End
ENSE00000931963	75236987	75237070
ENSE00001067025	75238513	75238636
ENSE00001067027	75242001	75242061
ENSE00001184534	75213705	75213793
ENSE00001184541	75213919	75213989
ENSE00001184546	75214605	75214678
ENSE00001184552	75215754	75215857
ENSE00001184557	75217866	75217960
ENSE00001184564	75218490	75218752
ENSE00001184571	75219257	75219344
ENSE00001184580	75219800	75219892
ENSE00001184587	75222361	75222460
ENSE00001184593	75227726	75227857
ENSE00001184603	75233986	75234098
ENSE00001453775	75202129	75203833
ENSE00001453785	75611040	75611114
ENSE00001678869	75211468	75211552
ENSE00003460645	75541435	75541516
ENSE00003483986	75300612	75300685
ENSE00003487330	75339582	75339630
ENSE00003495071	75251210	75251294
ENSE00003495608	75242886	75243011
ENSE00003500499	75396583	75396621
ENSE00003628780	75274958	75275042

Expression profiles

Bgee: expression breadth ubiquitous, 196 present calls, max score 90.47.

FANTOM5 (CAGE): breadth broad, TPM avg 2.2213 / max 155.1735, expressed in 447 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12875	1.0151	352
12873	0.7798	267
12876	0.2229	122
12874	0.1845	71
12872	0.0103	3
12871	0.0087	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	90.47	gold quality
ventricular zone	UBERON:0003053	83.03	gold quality
ganglionic eminence	UBERON:0004023	82.75	gold quality
skin of hip	UBERON:0001554	82.69	gold quality
endothelial cell	CL:0000115	81.93	gold quality
upper leg skin	UBERON:0004262	79.13	gold quality
tibia	UBERON:0000979	78.98	gold quality
primary visual cortex	UBERON:0002436	78.72	gold quality
upper arm skin	UBERON:0004263	78.72	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.63	gold quality
Brodmann (1909) area 23	UBERON:0013554	77.93	gold quality
gingival epithelium	UBERON:0001949	76.68	gold quality
oviduct epithelium	UBERON:0004804	74.96	gold quality
oral cavity	UBERON:0000167	73.98	gold quality
epithelial cell of pancreas	CL:0000083	73.52	silver quality
placenta	UBERON:0001987	73.31	gold quality
gingiva	UBERON:0001828	72.62	gold quality
skin of leg	UBERON:0001511	72.39	gold quality
islet of Langerhans	UBERON:0000006	72.11	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	71.86	gold quality
occipital lobe	UBERON:0002021	71.52	gold quality
deltoid	UBERON:0001476	71.49	silver quality
bronchial epithelial cell	CL:0002328	71.33	gold quality
right uterine tube	UBERON:0001302	71.32	gold quality
middle temporal gyrus	UBERON:0002771	71.13	silver quality
esophagus mucosa	UBERON:0002469	70.99	gold quality
zone of skin	UBERON:0000014	70.86	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.71	gold quality
germinal epithelium of ovary	UBERON:0001304	69.99	gold quality
bronchus	UBERON:0002185	69.94	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	82.79
E-HCAD-25	yes	36.75
E-ANND-3	yes	5.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting SLC44A5, 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-548C-3P	99.99	74.01	7587
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-4796-5P	99.34	70.06	810
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-513B-3P	98.76	68.12	1577
HSA-MIR-617	96.79	65.96	738
HSA-MIR-1236-5P	96.62	66.38	856
HSA-MIR-4714-3P	96.53	67.44	452
HSA-MIR-624-5P	96.00	68.88	728

Literature-anchored findings (GeneRIF, showing 1)

• the present study indicated the important role of SLC44A5 as a tumor promoter in HCC through the inhibition of choline uptake, suggesting that SLC44A5 may be a potential target for HCC therapy. (PMID:27082540)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc44a5a	ENSDARG00000017398
danio_rerio	slc44a5b	ENSDARG00000057419
mus_musculus	Slc44a5	ENSMUSG00000028360
rattus_norvegicus	Slc44a5	ENSRNOG00000042332

Paralogs (4): SLC44A1 (ENSG00000070214), SLC44A2 (ENSG00000129353), SLC44A3 (ENSG00000143036), SLC44A4 (ENSG00000204385)

Protein

Protein identifiers

Choline transporter-like protein 5 — Q8NCS7 (reviewed: Q8NCS7)

Alternative names: Solute carrier family 44 member 5

All UniProt accessions (1): Q8NCS7

UniProt curated annotations — full annotation on UniProt →

Function. Choline/H+ antiporter.

Subcellular location. Cell membrane.

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

Isoforms (3)

UniProt ID	Names	Canonical?
Q8NCS7-1	1, A	yes
Q8NCS7-4	2, B
Q8NCS7-5	3

RefSeq proteins (6): NP_001123530, NP_001307212, NP_001307214, NP_001307216, NP_001380993, NP_689910 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007603	Choline_transptr-like	Family

Pfam: PF04515

Catalyzed reactions (Rhea), 1 shown:

• choline(out) + n H(+)(in) = choline(in) + n H(+)(out) (RHEA:75463)

UniProt features (31 total): topological domain 11, transmembrane region 10, glycosylation site 3, sequence conflict 3, splice variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NCS7-F1	82.53	0.35

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 (3): 88, 190, 314

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: 110 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_BIOSYNTHETIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, TGACATY_UNKNOWN, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, GOBP_ORGANIC_CATION_TRANSPORT, GOBP_TRANSMEMBRANE_TRANSPORT, SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN

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

GO Molecular Function (4): choline transmembrane transporter activity (GO:0015220), antiporter activity (GO:0015297), 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
nitrogen compound transport	1
transport	1
cellular process	1
choline transport	1
transmembrane transporter activity	1
secondary active 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

718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC44A5	SLC5A7	Q9GZV3	534
SLC44A5	CIMIP7	H3BNL1	507
SLC44A5	DEFB107A	Q8IZN7	472
SLC44A5	SGCD	Q92629	438
SLC44A5	LHFPL3	Q86UP9	437
SLC44A5	ABCC2	Q92887	425
SLC44A5	SLC10A4	Q96EP9	372
SLC44A5	CD48	P09326	372
SLC44A5	SLC6A17	Q9H1V8	366
SLC44A5	NYAP2	Q9P242	363
SLC44A5	ZBBX	A8MT70	358
SLC44A5	PPT1	P50897	353
SLC44A5	SLC2A1	P11166	352
SLC44A5	OR51D1	Q8NGF3	349
SLC44A5	S100A3	P33764	339

IntAct

49 interactions, top by confidence:

A	B	Type	Score
SLC44A5	BDNF	psi-mi:“MI:0915”(physical association)	0.560
SLC44A5	SERPINH1	psi-mi:“MI:0915”(physical association)	0.560
SLC44A5	PECAM1	psi-mi:“MI:0915”(physical association)	0.560
SLC44A5	RAD23A	psi-mi:“MI:0915”(physical association)	0.560
SLC44A5	TGFBR2	psi-mi:“MI:0915”(physical association)	0.560
SLC44A5	CBX5	psi-mi:“MI:0915”(physical association)	0.560
SLC44A5	JPH3	psi-mi:“MI:0915”(physical association)	0.560
HTT	SLC44A5	psi-mi:“MI:0915”(physical association)	0.560
TARDBP	SLC44A5	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (110): RNF181 (Affinity Capture-MS), CLDND1 (Affinity Capture-MS), MOSPD2 (Affinity Capture-MS), REEP4 (Affinity Capture-MS), SLC44A5 (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), ATG9A (Affinity Capture-MS), TMEM63A (Affinity Capture-MS), SLC44A5 (Proximity Label-MS), SLC44A5 (Proximity Label-MS), CLDND1 (Affinity Capture-MS), RNF181 (Affinity Capture-MS), SLC44A5 (Affinity Capture-MS), REEP4 (Affinity Capture-MS), SLC44A5 (Affinity Capture-MS)

ESM2 similar proteins: A3KMY4, A4FUZ5, A5PF08, A5PMW0, A8XKF2, B0S5A7, B5X3W7, O88407, O97704, P55019, P59158, Q06496, Q13530, Q14AT5, Q17JQ7, Q1LZ71, Q20026, Q28620, Q4R6L9, Q53GD3, Q58CW5, Q5R4I4, Q5R533, Q5R5L9, Q5RJI2, Q60825, Q63175, Q6GN42, Q6IFT6, Q6MG71, Q6T3U3, Q6T3U4, Q7PRJ0, Q7Q5R7, Q7SYC9, Q7T2B0, Q803X0, Q86VE9, Q8BHJ6, Q8K097

Diamond homologs: A3KMY4, A5D7H3, A5PF08, A5PMW0, A8XKF2, B0JZD0, B0S5A7, B4F795, B5X3W7, F1S584, Q20026, Q53GD3, Q54I48, Q5R5L9, Q5RJI2, Q6GN42, Q6IP59, Q6MG71, Q7PRJ0, Q7SYC9, Q7T2B0, Q810F1, Q8BY89, Q8IWA5, Q8NCS7, Q91VA1, Q95JW2, Q9VAP3, Q4I8E9, Q6C938, Q6IR74, Q869R1, Q8N4M1, Q8WWI5, A5PK40, Q6AY92, Q54IJ2, Q9I9B9, Q12412, Q5AB93

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4393 predictions. Top by Δscore:

Variant	Effect	Δscore
1:75213998:C:CT	acceptor_gain	1.0000
1:75213999:A:T	acceptor_gain	1.0000
1:75215750:CTA:C	donor_loss	1.0000
1:75215751:TA:T	donor_loss	1.0000
1:75219385:T:TC	acceptor_gain	1.0000
1:75222360:CTTG:C	donor_gain	1.0000
1:75222459:CACTT:C	acceptor_gain	1.0000
1:75227724:A:AC	donor_gain	1.0000
1:75227725:C:CA	donor_gain	1.0000
1:75227725:CT:C	donor_gain	1.0000
1:75227725:CTA:C	donor_gain	1.0000
1:75227725:CTAA:C	donor_gain	1.0000
1:75227725:CTAAA:C	donor_gain	1.0000
1:75227856:TCC:T	acceptor_loss	1.0000
1:75227857:CCT:C	acceptor_gain	1.0000
1:75227858:CTTG:C	acceptor_loss	1.0000
1:75227859:T:C	acceptor_gain	1.0000
1:75227859:T:TC	acceptor_gain	1.0000
1:75234099:C:CC	acceptor_gain	1.0000
1:75236980:CACTT:C	donor_loss	1.0000
1:75236981:ACTT:A	donor_loss	1.0000
1:75236982:CTTAC:C	donor_loss	1.0000
1:75236983:TTACA:T	donor_loss	1.0000
1:75236984:TACAT:T	donor_loss	1.0000
1:75236985:A:AC	donor_gain	1.0000
1:75236985:ACA:A	donor_loss	1.0000
1:75236986:C:CA	donor_gain	1.0000
1:75236986:C:T	donor_loss	1.0000
1:75236986:CA:C	donor_gain	1.0000
1:75236986:CAT:C	donor_gain	1.0000

AlphaMissense

4724 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:75234071:A:C	S256R	0.997
1:75234071:A:T	S256R	0.997
1:75234073:T:G	S256R	0.997
1:75217949:C:T	G514E	0.996
1:75218623:A:G	W466R	0.996
1:75218623:A:T	W466R	0.996
1:75274982:C:G	C79S	0.996
1:75274983:A:T	C79S	0.996
1:75217946:G:A	S515F	0.995
1:75211472:G:C	C681W	0.994
1:75217934:C:T	G519E	0.994
1:75238624:C:G	C182S	0.994
1:75238625:A:T	C182S	0.994
1:75243007:C:G	C117S	0.994
1:75243008:A:T	C117S	0.994
1:75218706:C:G	C438S	0.993
1:75218707:A:T	C438S	0.993
1:75242995:C:G	C121S	0.992
1:75242996:A:T	C121S	0.992
1:75211474:A:G	C681R	0.991
1:75237018:C:G	D237H	0.991
1:75214665:C:A	G581V	0.990
1:75217946:G:T	S515Y	0.990
1:75217950:C:G	G514R	0.990
1:75217950:C:T	G514R	0.990
1:75218570:G:C	F483L	0.990
1:75218570:G:T	F483L	0.990
1:75218572:A:G	F483L	0.990
1:75238625:A:G	C182R	0.990
1:75213919:C:G	G625R	0.989

dbSNP variants (sampled 300 via entrez): RS1000010915 (1:75565185 C>A), RS1000017997 (1:75644700 T>C), RS1000032004 (1:75553583 C>T), RS1000035455 (1:75280596 A>T), RS1000041484 (1:75638010 C>T), RS1000044295 (1:75468877 C>T), RS1000045904 (1:75430258 C>A,T), RS1000048177 (1:75423974 G>A), RS1000053129 (1:75295800 C>T), RS1000055716 (1:75235771 C>T), RS1000055871 (1:75697286 T>C), RS1000056368 (1:75205406 C>A,T), RS1000073981 (1:75242740 A>G), RS1000077273 (1:75383795 G>A), RS1000095166 (1:75655230 C>T)

Disease associations

OMIM: gene MIM:620329 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST000895_1	Whole-brain volume (Alzheimer’s disease interaction)	2.000000e-06
GCST001368_2	Capecitabine sensitivity	7.000000e-06
GCST004158_3	Self-reported tiredness	6.000000e-08
GCST005648_33	Serum metabolite concentrations in chronic kidney disease	1.000000e-12
GCST005650_211	Serum metabolite ratios in chronic kidney disease	2.000000e-18
GCST005650_212	Serum metabolite ratios in chronic kidney disease	4.000000e-30
GCST012020_226	Serum metabolite levels	5.000000e-15

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005089	whole-brain volume
EFO:0007946	tiredness 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 — SLC44 choline transporter-like family

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
trichostatin A	affects cotreatment, increases expression	3
Benzo(a)pyrene	increases expression, increases methylation, increases mutagenesis, affects methylation	3
Aflatoxin B1	affects expression, decreases methylation, increases expression	3
Nickel	decreases expression	2
Tretinoin	increases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
uranyl acetate	affects expression	1
propionaldehyde	increases expression	1
bisphenol A	decreases methylation	1
terbufos	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cupric chloride	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
jinfukang	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Cadmium	increases response to substance, increases expression	1
Calcitriol	increases expression	1
Cisplatin	increases expression	1
Demecolcine	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	affects expression	1
Fonofos	increases methylation	1
Ethyl Methanesulfonate	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4TT	HuH7-SLC44A5-KO-c3	Cancer cell line	Male
CVCL_D4TU	HuH7-SLC44A5-KO-c5	Cancer cell line	Male

Clinical trials (associated diseases)

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