SLC35F3

Summary

SLC35F3 (solute carrier family 35 member F3, HGNC:23616) is a protein-coding gene on chromosome 1q42.2, encoding Solute carrier family 35 member F3 (Q8IY50). Mediates thiamine transport.

Involved in thiamine transport. Predicted to be located in membrane.

Source: NCBI Gene 148641 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 79 total — 1 pathogenic
• MANE Select transcript: NM_173508

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23616
Approved symbol	SLC35F3
Name	solute carrier family 35 member F3
Location	1q42.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37712
Ensembl gene	ENSG00000183780
Ensembl biotype	protein_coding
Entrez	148641

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000366617, ENST00000366618

RefSeq mRNA: 2 — MANE Select: NM_173508 NM_001300845, NM_173508

CCDS: CCDS1600, CCDS73050

Canonical transcript exons

ENST00000366618 — 8 exons

Exon	Start	End
ENSE00001302858	234231417	234231741
ENSE00001306170	234309101	234309320
ENSE00001307980	234320098	234320187
ENSE00001325123	233905529	233905758
ENSE00001326066	234316602	234316727
ENSE00001330490	234318751	234318943
ENSE00001442184	233904676	233905130
ENSE00001509906	234323008	234324511

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 83.41.

FANTOM5 (CAGE): breadth broad, TPM avg 2.5007 / max 106.3283, expressed in 584 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9107	1.3649	322
9102	1.1308	389
9101	0.0051	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	83.41	gold quality
middle temporal gyrus	UBERON:0002771	83.03	gold quality
cerebellar hemisphere	UBERON:0002245	82.42	gold quality
cerebellar cortex	UBERON:0002129	82.36	gold quality
cerebellum	UBERON:0002037	82.12	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.97	gold quality
prefrontal cortex	UBERON:0000451	80.72	gold quality
superior frontal gyrus	UBERON:0002661	80.61	gold quality
Brodmann (1909) area 46	UBERON:0006483	80.37	gold quality
primary visual cortex	UBERON:0002436	80.36	gold quality
postcentral gyrus	UBERON:0002581	80.34	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.86	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	79.26	gold quality
frontal cortex	UBERON:0001870	79.13	gold quality
islet of Langerhans	UBERON:0000006	79.07	gold quality
cerebellar vermis	UBERON:0004720	78.38	gold quality
neocortex	UBERON:0001950	78.06	gold quality
parietal lobe	UBERON:0001872	77.64	gold quality
nucleus accumbens	UBERON:0001882	77.53	gold quality
right frontal lobe	UBERON:0002810	77.44	gold quality
anterior cingulate cortex	UBERON:0009835	77.22	gold quality
stromal cell of endometrium	CL:0002255	77.10	gold quality
cerebral cortex	UBERON:0000956	76.80	gold quality
caudate nucleus	UBERON:0001873	76.68	gold quality
occipital lobe	UBERON:0002021	75.89	gold quality
putamen	UBERON:0001874	75.78	gold quality
brain	UBERON:0000955	74.51	gold quality
forebrain	UBERON:0001890	74.34	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.19	gold quality
Ammon’s horn	UBERON:0001954	73.02	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	4149.40
E-CURD-119	yes	24.88
E-ANND-3	yes	4.24

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

87 targeting SLC35F3, 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-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
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-4789-3P	99.99	70.75	2484
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc35f3b	ENSDARG00000059850
danio_rerio	slc35f3a	ENSDARG00000075909
mus_musculus	Slc35f3	ENSMUSG00000057060
rattus_norvegicus	Slc35f3	ENSRNOG00000049456
drosophila_melanogaster	CG42322	FBGN0259222
caenorhabditis_elegans		WBGENE00022252

Paralogs (1): SLC35F4 (ENSG00000151812)

Protein

Protein identifiers

Solute carrier family 35 member F3 — Q8IY50 (reviewed: Q8IY50)

Alternative names: Thiamine transporter SLC35F3

All UniProt accessions (1): Q8IY50

UniProt curated annotations — full annotation on UniProt →

Function. Mediates thiamine transport.

Subcellular location. Membrane.

Tissue specificity. Expressed at the highest levels in the adult cerebellum.

Polymorphism. Individuals with blood hypertension and a SLC35F3 risk allele T/T homozygosity (intronic variant rs17514104) show a significant reduction in blood thiamine content.

Similarity. Belongs to the SLC35F solute transporter family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IY50-1	1	yes
Q8IY50-2	2

RefSeq proteins (2): NP_001287774, NP_775779* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000620	EamA_dom	Domain
IPR026505	Solute_c_fam_35_mem_F3/F4	Family
IPR037185	EmrE-like	Homologous_superfamily

Pfam: PF00892

Catalyzed reactions (Rhea), 1 shown:

• thiamine(in) = thiamine(out) (RHEA:34919)

UniProt features (16 total): transmembrane region 10, region of interest 2, chain 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IY50-F1	75.68	0.29

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_SULFUR_COMPOUND_TRANSPORT, GOBP_VITAMIN_TRANSPORT, RICKMAN_HEAD_AND_NECK_CANCER_A, GOBP_ORGANIC_CATION_TRANSPORT, GEORGES_TARGETS_OF_MIR192_AND_MIR215, MEISSNER_NPC_HCP_WITH_H3K4ME2, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, FORTSCHEGGER_PHF8_TARGETS_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, FOXN3_TARGET_GENES, ZNF596_TARGET_GENES, ZNF610_TARGET_GENES, MIR607

GO Biological Process (1): thiamine transport (GO:0015888)

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
vitamin transport	1
nitrogen compound transport	1
sulfur compound transport	1
cellular anatomical structure	1

Protein interactions and networks

STRING

834 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC35F3	SLC35H1	Q9NQQ7	552
SLC35F3	SLC35D1	Q9NTN3	528
SLC35F3	FAM185A	Q8N0U4	479
SLC35F3	SLC35E3	Q7Z769	476
SLC35F3	SLC35F2	Q8IXU6	459
SLC35F3	SLC35C1	Q96A29	441
SLC35F3	SLC35A1	P78382	432
SLC35F3	IER5L	Q5T953	425
SLC35F3	ZNF804B	A4D1E1	420
SLC35F3	STOML3	Q8TAV4	411
SLC35F3	SLC35G2	Q8TBE7	394
SLC35F3	SLC35B3	Q9H1N7	379
SLC35F3	NALF1	B1AL88	375
SLC35F3	SLC39A2	Q9NP94	372
SLC35F3	TMEM179	Q6ZVK1	370

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SLC35F3	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLC35G5	SLC35G6	psi-mi:“MI:0914”(association)	0.350

BioGRID (108): SLC35F3 (Affinity Capture-MS), SLC35F3 (Affinity Capture-RNA), SLC35F3 (Affinity Capture-MS), SLC35F3 (Affinity Capture-MS), ABCB10 (Affinity Capture-MS), ACAD9 (Affinity Capture-MS), ACBD3 (Affinity Capture-MS), ADAM9 (Affinity Capture-MS), GPR64 (Affinity Capture-MS), LPHN2 (Affinity Capture-MS), ADPGK (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANO10 (Affinity Capture-MS), ASIC1 (Affinity Capture-MS), ATP13A1 (Affinity Capture-MS)

ESM2 similar proteins: A1L272, A2RV80, A4IF30, A6QL92, A6QPI1, O02777, O80605, P17200, P20272, P21554, P47746, P51810, P56971, P70259, Q1LZI2, Q2V4F9, Q3TDN0, Q3UGM2, Q4R794, Q5F383, Q5FVJ3, Q5IS73, Q5R4D7, Q5R6J3, Q5RD30, Q66H88, Q6P0E8, Q6P499, Q6R5J2, Q71SP5, Q8BGN5, Q8BZK4, Q8CBH5, Q8IY50, Q8NA31, Q8NBV4, Q8R314, Q8RWF4, Q8WV83, Q91WB2

Diamond homologs: A4IF30, Q1LZI2, Q8BZK4, Q8IY50

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	63
Likely benign	4
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1180519	GRCh37/hg19 1q42.2-43(chr1:231407943-237289859)x1	Pathogenic

SpliceAI

3791 predictions. Top by Δscore:

Variant	Effect	Δscore
1:233905126:GCCGT:G	donor_gain	1.0000
1:233905129:GT:G	donor_gain	1.0000
1:233905759:G:GG	donor_gain	1.0000
1:233910095:G:GT	donor_gain	1.0000
1:234024617:GAGC:G	donor_gain	1.0000
1:234024620:C:G	donor_gain	1.0000
1:234257582:G:GT	donor_gain	1.0000
1:234309095:TTTTA:T	acceptor_loss	1.0000
1:234309096:TTTAG:T	acceptor_loss	1.0000
1:234309097:TTAG:T	acceptor_loss	1.0000
1:234309098:TAGGG:T	acceptor_loss	1.0000
1:234309099:A:T	acceptor_loss	1.0000
1:234309099:AG:A	acceptor_gain	1.0000
1:234309099:AGG:A	acceptor_gain	1.0000
1:234309100:GG:G	acceptor_gain	1.0000
1:234309100:GGG:G	acceptor_gain	1.0000
1:234309100:GGGA:G	acceptor_gain	1.0000
1:234309319:GG:G	donor_gain	1.0000
1:234309320:GG:G	donor_gain	1.0000
1:234316598:CCAG:C	acceptor_loss	1.0000
1:234316599:CAGAT:C	acceptor_loss	1.0000
1:234316600:A:AG	acceptor_gain	1.0000
1:234316600:AGATT:A	acceptor_gain	1.0000
1:234316601:G:GA	acceptor_gain	1.0000
1:234316601:GA:G	acceptor_gain	1.0000
1:234316601:GATT:G	acceptor_gain	1.0000
1:234316601:GATTG:G	acceptor_gain	1.0000
1:234316724:CAAGG:C	donor_loss	1.0000
1:234316725:AAGGT:A	donor_loss	1.0000
1:234316726:AGG:A	donor_loss	1.0000

AlphaMissense

3183 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:234316629:G:C	G217R	0.999
1:234309285:T:A	W196R	0.998
1:234309285:T:C	W196R	0.998
1:234309306:T:C	F203L	0.998
1:234309307:T:C	F203S	0.998
1:234309308:C:A	F203L	0.998
1:234309308:C:G	F203L	0.998
1:234316630:G:A	G217D	0.998
1:234231644:T:A	W102R	0.997
1:234231644:T:C	W102R	0.997
1:234316717:C:A	A246D	0.997
1:234320169:A:C	S338R	0.997
1:234320171:C:A	S338R	0.997
1:234320171:C:G	S338R	0.997
1:234323079:G:C	G368R	0.997
1:234309273:T:C	F192L	0.996
1:234309275:C:A	F192L	0.996
1:234309275:C:G	F192L	0.996
1:234309280:T:C	L194P	0.996
1:234309292:T:A	V198D	0.996
1:234309295:T:C	L199P	0.996
1:234309307:T:G	F203C	0.996
1:234316609:C:A	A210D	0.996
1:234316705:C:A	A242E	0.996
1:234309255:T:C	C186R	0.995
1:234309282:T:C	S195P	0.995
1:234309312:G:A	G205R	0.995
1:234309312:G:C	G205R	0.995
1:234316629:G:T	G217C	0.995
1:234316630:G:T	G217V	0.995

dbSNP variants (sampled 300 via entrez): RS1000022366 (1:233968677 G>A), RS1000049168 (1:234004030 G>A), RS1000053797 (1:233995726 G>A), RS1000059931 (1:234017333 A>G), RS1000082166 (1:234266297 G>T), RS1000093793 (1:234232281 T>A,C), RS1000094134 (1:234059333 G>A,C), RS1000094779 (1:234211290 C>A), RS1000127461 (1:233992435 G>A), RS1000130701 (1:233983047 C>T), RS1000134538 (1:234265980 T>C), RS1000142780 (1:234098066 GGTA>G), RS1000149460 (1:234232447 G>A), RS1000152303 (1:234206680 G>A), RS1000153456 (1:234163007 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST003264_447	Post bronchodilator FEV1/FVC ratio	7.000000e-07
GCST004214_2	Creatinine levels	1.000000e-08
GCST004735_2	Epstein-Barr virus copy number in lymphoblastoid cell lines	1.000000e-06
GCST005576_1	Intracranial aneurysm	8.000000e-07
GCST006479_105	Diverticular disease	4.000000e-22
GCST007611_3	Chronic obstructive pulmonary disease or high blood pressure (pleiotropy)	5.000000e-08
GCST008154_10	Trunk fat mass	7.000000e-07
GCST009364_28	Triglyceride levels x long total sleep time interaction (2df test)	5.000000e-09
GCST010579_2	Response to antiepileptic mood-stabilizing treatment in bipolar disorder	3.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004713	FEV/FVC ratio
EFO:0009959	diverticular disease
EFO:0004530	triglyceride 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 — SLC35 family of nucleotide sugar transporters

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression, increases methylation	3
sodium arsenite	increases expression, decreases expression	2
Resveratrol	affects cotreatment, decreases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
fluorene-9-bisphenol	increases expression	1
propionaldehyde	increases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	affects cotreatment, increases methylation	1
arsenite	increases methylation	1
perfluorooctanoic acid	decreases expression	1
zinc chromate	increases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
perfluorohexanesulfonic acid	decreases expression	1
belinostat	decreases expression	1
abrine	increases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
jinfukang	affects cotreatment, decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Copper	affects cotreatment, decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	decreases 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_D4MJ	HCT116-SLC35F3-KO-c2	Cancer cell line	Male
CVCL_D4MK	HCT116-SLC35F3-KO-c3	Cancer cell line	Male

Clinical trials (associated diseases)

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