SLC35F1

Summary

SLC35F1 (solute carrier family 35 member F1, HGNC:21483) is a protein-coding gene on chromosome 6q22.2-q22.31, encoding Solute carrier family 35 member F1 (Q5T1Q4). Putative solute transporter.

Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Located in synaptic vesicle membrane.

Source: NCBI Gene 222553 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder (Moderate, GenCC)
• GWAS associations: 147
• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_001029858

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21483
Approved symbol	SLC35F1
Name	solute carrier family 35 member F1
Location	6q22.2-q22.31
Locus type	gene with protein product
Status	Approved
Aliases	dJ230I3.1
Ensembl gene	ENSG00000196376
Ensembl biotype	protein_coding
OMIM	620349
Entrez	222553

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000360388, ENST00000621341

RefSeq mRNA: 2 — MANE Select: NM_001029858 NM_001029858, NM_001415931

CCDS: CCDS34524

Canonical transcript exons

ENST00000360388 — 8 exons

Exon	Start	End
ENSE00000840043	118266995	118267154
ENSE00001406000	118154445	118154620
ENSE00001407799	118235509	118235636
ENSE00001447270	117907264	117907899
ENSE00002282818	118277494	118277546
ENSE00002283580	118285184	118285338
ENSE00002298981	118275459	118275615
ENSE00003846240	118314028	118317671

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 97.69.

FANTOM5 (CAGE): breadth broad, TPM avg 4.0644 / max 134.6507, expressed in 399 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
69457	3.2503	384
69458	0.3922	168
69459	0.1984	105
69456	0.1392	90
204174	0.0843	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	97.69	gold quality
endothelial cell	CL:0000115	97.56	gold quality
Brodmann (1909) area 46	UBERON:0006483	95.68	gold quality
buccal mucosa cell	CL:0002336	95.53	gold quality
dorsal root ganglion	UBERON:0000044	94.52	gold quality
parietal lobe	UBERON:0001872	93.95	gold quality
middle temporal gyrus	UBERON:0002771	93.77	gold quality
postcentral gyrus	UBERON:0002581	93.74	gold quality
superior frontal gyrus	UBERON:0002661	93.71	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.70	gold quality
cortical plate	UBERON:0005343	93.35	gold quality
trigeminal ganglion	UBERON:0001675	92.19	gold quality
ganglionic eminence	UBERON:0004023	91.80	gold quality
entorhinal cortex	UBERON:0002728	91.66	gold quality
substantia nigra pars compacta	UBERON:0001965	90.84	gold quality
occipital lobe	UBERON:0002021	90.78	gold quality
primary visual cortex	UBERON:0002436	89.80	gold quality
left ventricle myocardium	UBERON:0006566	89.70	gold quality
substantia nigra pars reticulata	UBERON:0001966	89.38	gold quality
prefrontal cortex	UBERON:0000451	89.20	gold quality
temporal lobe	UBERON:0001871	88.90	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.90	gold quality
neocortex	UBERON:0001950	88.44	gold quality
cerebral cortex	UBERON:0000956	88.37	gold quality
frontal cortex	UBERON:0001870	88.18	gold quality
anterior cingulate cortex	UBERON:0009835	87.95	gold quality
lateral globus pallidus	UBERON:0002476	87.86	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.30	gold quality
ventral tegmental area	UBERON:0002691	86.98	gold quality
amygdala	UBERON:0001876	86.84	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-180759	yes	2786.25
E-GEOD-84465	yes	519.34
E-HCAD-35	yes	84.32
E-HCAD-25	yes	23.91
E-ENAD-20	no	261.04
E-ANND-3	no	4.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

232 targeting SLC35F1, 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-3613-3P	100.00	76.36	7965
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-513A-5P	100.00	69.77	2465
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394

Literature-anchored findings (GeneRIF, showing 2)

• SLC35F1 as a candidate gene for neurodevelopmental disorders resembling Rett syndrome. (PMID:33821533)
• Residence of the Nucleotide Sugar Transporter Family Members SLC35F1 and SLC35F6 in the Endosomal/Lysosomal Pathway. (PMID:38928424)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc35f1	ENSDARG00000053003
mus_musculus	Slc35f1	ENSMUSG00000038602
rattus_norvegicus	Slc35f1	ENSRNOG00000000412
caenorhabditis_elegans	Y73E7A.3	WBGENE00022270

Paralogs (1): SLC35F2 (ENSG00000110660)

Protein

Protein identifiers

Solute carrier family 35 member F1 — Q5T1Q4 (reviewed: Q5T1Q4)

All UniProt accessions (1): Q5T1Q4

UniProt curated annotations — full annotation on UniProt →

Function. Putative solute transporter.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle membrane.

Similarity. Belongs to the SLC35F solute transporter family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5T1Q4-1	1	yes
Q5T1Q4-2	2

RefSeq proteins (2): NP_001025029, NP_001402860 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009262	SLC35_F1/F2/F6	Family
IPR037185	EmrE-like	Homologous_superfamily
IPR052221	SLC35F_Transporter	Family

Pfam: PF06027

UniProt features (17 total): transmembrane region 10, sequence conflict 4, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T1Q4-F1	78.53	0.53

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 142 (showing top): TTTGTAG_MIR520D, AAGCCAT_MIR135A_MIR135B, CACCAGC_MIR138, CTAGGAA_MIR384, KOYAMA_SEMA3B_TARGETS_UP, ACATTCC_MIR1_MIR206, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, TTTGCAC_MIR19A_MIR19B, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_EXOCYTIC_VESICLE, GOCC_SECRETORY_VESICLE, GOCC_SYNAPSE, GOCC_PRESYNAPSE, GOCC_TRANSPORT_VESICLE_MEMBRANE, chr6q22

GO Biological Process (1): transmembrane transport (GO:0055085)

GO Molecular Function (2): transmembrane transporter activity (GO:0022857), protein binding (GO:0005515)

GO Cellular Component (4): synaptic vesicle membrane (GO:0030672), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
transporter activity	1
transmembrane transport	1
binding	1
synaptic vesicle	1
exocytic vesicle membrane	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1
cell junction	1

Protein interactions and networks

STRING

1424 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC35F1	CEP85L	Q5SZL2	602
SLC35F1	SLC35E1	Q96K37	584
SLC35F1	CCDC141	Q6ZP82	574
SLC35F1	SLC35D3	Q5M8T2	568
SLC35F1	SLC35H1	Q9NQQ7	544
SLC35F1	SLC35A5	Q9BS91	543
SLC35F1	SLC35D1	Q9NTN3	531
SLC35F1	SLC35B1	P78383	531
SLC35F1	SLC35B4	Q969S0	528
SLC35F1	DCBLD1	Q8N8Z6	524
SLC35F1	SLC35D2	Q76EJ3	503
SLC35F1	RNF207	Q6ZRF8	500
SLC35F1	SLC35B3	Q9H1N7	493
SLC35F1	KIAA1755	Q5JYT7	490
SLC35F1	SLC35A1	P78382	476

IntAct

38 interactions, top by confidence:

A	B	Type	Score
SLC35F1	ATP5F1B	psi-mi:“MI:0915”(physical association)	0.690
TUSC5	SLC35F1	psi-mi:“MI:0915”(physical association)	0.560
GJA5	SLC35F1	psi-mi:“MI:0915”(physical association)	0.560
AQP6	SLC35F1	psi-mi:“MI:0915”(physical association)	0.560
SLC35F1	SLC35C2	psi-mi:“MI:0915”(physical association)	0.560
COMT	SLC35F1	psi-mi:“MI:0915”(physical association)	0.560
SLC35F1	TMEM14B	psi-mi:“MI:0915”(physical association)	0.560
GJA8	SLC35F1	psi-mi:“MI:0915”(physical association)	0.560
HTR2C	KLRG2	psi-mi:“MI:0914”(association)	0.530
NPY2R	RTL8C	psi-mi:“MI:0914”(association)	0.530
ATP5PF	SLC19A2	psi-mi:“MI:0914”(association)	0.530
VIPR2	C15orf61	psi-mi:“MI:0914”(association)	0.350
M	TM9SF1	psi-mi:“MI:0914”(association)	0.350
TTYH1	TMEM223	psi-mi:“MI:0914”(association)	0.350
BSCL2	TMEM223	psi-mi:“MI:0914”(association)	0.350
AVPR2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
C5AR1	TCAF2	psi-mi:“MI:0914”(association)	0.350
VIPR2	RABGAP1L	psi-mi:“MI:0914”(association)	0.350
TMEM169	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC35F1	C15orf61	psi-mi:“MI:0914”(association)	0.350
TUSC5	SLC35F1	psi-mi:“MI:0915”(physical association)	0.000
SLC35F1	GJA5	psi-mi:“MI:0915”(physical association)	0.000
SLC35F1	AQP6	psi-mi:“MI:0915”(physical association)	0.000
SLC35F1	SLC35C2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (157): SLC35F1 (Affinity Capture-MS), SLC35F1 (Affinity Capture-MS), ATP5B (Affinity Capture-MS), SLC35F1 (Affinity Capture-MS), SLC35F1 (Two-hybrid), SLC35F1 (Two-hybrid), SLC35F1 (Two-hybrid), SLC35F1 (Two-hybrid), SLC35F1 (Two-hybrid), SLC35F1 (Two-hybrid), GJA5 (Two-hybrid), SLC35F1 (Affinity Capture-MS), SLC35F1 (Affinity Capture-MS), SLC35F1 (Affinity Capture-MS), SLC35F1 (Affinity Capture-MS)

ESM2 similar proteins: A0NGI1, A7YW81, O74750, O94654, P40004, Q00974, Q02334, Q03730, Q04083, Q09875, Q0D2K0, Q0V9U2, Q10000, Q29Q28, Q3E6T0, Q3SWX0, Q54V96, Q54ZG7, Q550W6, Q55FV8, Q5R7Q3, Q5T1Q4, Q6CR04, Q6FSF8, Q7RTP0, Q7TML3, Q8BGK5, Q8BHK1, Q8BLX4, Q8BMW7, Q8BZF2, Q8IXU6, Q8MXJ9, Q8N8Q9, Q8R1E7, Q8WY98, Q94EI9, Q968A5, Q9C8M1, Q9JJC8

Diamond homologs: O59785, Q0V9U2, Q5T1Q4, Q7TML3, Q8BGK5, Q8IXU6, Q550A6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3940 predictions. Top by Δscore:

Variant	Effect	Δscore
6:117907898:AGGT:A	donor_loss	1.0000
6:117907899:GGTG:G	donor_loss	1.0000
6:117907900:GTGA:G	donor_loss	1.0000
6:118046022:A:T	donor_gain	1.0000
6:118095364:C:T	donor_gain	1.0000
6:118235502:A:AG	acceptor_gain	1.0000
6:118235503:A:G	acceptor_gain	1.0000
6:118235506:CAG:C	acceptor_loss	1.0000
6:118235507:A:AG	acceptor_gain	1.0000
6:118235507:AGG:A	acceptor_loss	1.0000
6:118235508:G:GG	acceptor_gain	1.0000
6:118235508:GGA:G	acceptor_gain	1.0000
6:118235596:TGGTC:T	donor_gain	1.0000
6:118235630:TATCC:T	donor_gain	1.0000
6:118235631:ATCCA:A	donor_gain	1.0000
6:118235632:TCCAG:T	donor_gain	1.0000
6:118235635:AG:A	donor_loss	1.0000
6:118235636:GG:G	donor_loss	1.0000
6:118235637:G:T	donor_loss	1.0000
6:118235638:T:A	donor_loss	1.0000
6:118275445:T:TA	acceptor_gain	1.0000
6:118275613:ATT:A	donor_gain	1.0000
6:118275613:ATTGT:A	donor_loss	1.0000
6:118275614:TT:T	donor_gain	1.0000
6:118275614:TTGTG:T	donor_loss	1.0000
6:118275615:TGTG:T	donor_loss	1.0000
6:118275616:G:GG	donor_gain	1.0000
6:118275616:GTG:G	donor_loss	1.0000
6:118275617:TGA:T	donor_loss	1.0000
6:118275618:GAG:G	donor_loss	1.0000

AlphaMissense

2609 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:118275572:G:A	G251R	0.998
6:118275572:G:C	G251R	0.998
6:118275573:G:A	G251E	0.998
6:118275581:G:C	G254R	0.998
6:118275582:G:A	G254D	0.998
6:118285228:A:C	S298R	0.998
6:118285230:C:A	S298R	0.998
6:118285230:C:G	S298R	0.998
6:118154606:T:C	L112P	0.997
6:118314071:G:A	G349E	0.997
6:118154609:C:A	A113D	0.996
6:118275602:A:C	S261R	0.996
6:118275604:T:A	S261R	0.996
6:118275604:T:G	S261R	0.996
6:118314070:G:A	G349R	0.996
6:118314070:G:C	G349R	0.996
6:118235544:T:A	W129R	0.995
6:118235544:T:C	W129R	0.995
6:118235565:G:A	G136R	0.995
6:118235565:G:C	G136R	0.995
6:118235604:G:C	A149P	0.995
6:118267091:T:C	C192R	0.995
6:118275512:G:C	G231R	0.995
6:118275606:G:A	G262E	0.995
6:118285204:A:C	S290R	0.995
6:118285206:T:A	S290R	0.995
6:118285206:T:G	S290R	0.995
6:118235553:T:C	Y132H	0.994
6:118267079:G:C	G188R	0.994
6:118267080:G:A	G188D	0.994

dbSNP variants (sampled 300 via entrez): RS1000008793 (6:118315168 G>C), RS1000014651 (6:118299517 A>C,T), RS1000017684 (6:117984424 C>G,T), RS1000018783 (6:117951187 A>C), RS1000022040 (6:118228948 T>C), RS1000025159 (6:118187823 A>G), RS1000027984 (6:118184975 T>C), RS1000032851 (6:118057844 G>C), RS1000038469 (6:118099838 T>C), RS1000055598 (6:118142689 G>A), RS1000063501 (6:118186570 C>T), RS1000073250 (6:117998867 T>C), RS1000089002 (6:118177593 G>A), RS1000096759 (6:117965551 C>T), RS1000098197 (6:118088678 G>C,T)

Disease associations

OMIM: gene MIM:620349 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder	Moderate	Autosomal dominant

Mondo (2): nephrotic syndrome (MONDO:0005377), neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

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

GWAS associations

147 associations (top):

Study	Trait	p-value
GCST000363_13	QT interval	5.000000e-22
GCST000441_1	Cardiac structure and function	1.000000e-09
GCST000444_2	QT interval	2.000000e-29
GCST000731_1	Resting heart rate	4.000000e-10
GCST001859_40	Thiazide-induced adverse metabolic effects in hypertensive patients	4.000000e-06
GCST001969_11	Heart rate	8.000000e-21
GCST002500_55	QT interval	3.000000e-18
GCST002500_56	QT interval	1.000000e-22
GCST002500_57	QT interval	2.000000e-67
GCST002500_58	QT interval	8.000000e-16
GCST002500_59	QT interval	1.000000e-08
GCST003844_31	QRS duration	8.000000e-29
GCST004280_12	Diastolic blood pressure	2.000000e-11
GCST004297_5	Atrial fibrillation	1.000000e-08
GCST005171_24	QT interval	2.000000e-13
GCST006061_140	Atrial fibrillation	4.000000e-16
GCST006414_118	Atrial fibrillation	2.000000e-22
GCST007094_99	Diastolic blood pressure	3.000000e-09
GCST007099_209	Systolic blood pressure	2.000000e-06
GCST007218_10	QT interval	2.000000e-35
GCST007227_1	QRS duration	3.000000e-30
GCST010321_116	PR interval	3.000000e-54
GCST010346_24	TPE interval (resting)	2.000000e-13
GCST010346_40	TPE interval (resting)	5.000000e-26
GCST010346_7	TPE interval (resting)	3.000000e-14
GCST010796_2399	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-08
GCST010796_2400	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-09
GCST010796_2601	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-09
GCST010796_4901	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-16
GCST010796_4902	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-16

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004682	QT interval
EFO:0004298	cardiovascular measurement
EFO:0004530	triglyceride measurement
EFO:0005054	QRS complex
EFO:0006336	diastolic blood pressure
EFO:0006335	systolic blood pressure
EFO:0004462	PR interval
EFO:0004644	TPE interval measurement
EFO:0004327	electrocardiography

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D009404	Nephrotic Syndrome	C12.050.351.968.419.630.643; C12.200.777.419.630.643; C12.950.419.630.643
D065886	Neurodevelopmental Disorders	F03.625

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

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	increases expression	2
Nickel	decreases expression	2
Valproic Acid	increases methylation, affects expression	2
OTX015	increases expression	1
mivebresib	increases expression	1
bisphenol A	affects methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
abrine	increases expression	1
bisphenol S	decreases methylation	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Ethanol	increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Doxorubicin	decreases expression	1
Lead	affects expression	1
Lipopolysaccharides	increases expression, affects response to substance	1
Tretinoin	decreases expression	1
Triclosan	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_TN25	HAP1 SLC35F1 (-) 1	Cancer cell line	Male
CVCL_TN26	HAP1 SLC35F1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT00308321	PHASE4	UNKNOWN	Long Term Tapering or Standard Steroids for Nephrotic Syndrome
NCT01021540	PHASE4	COMPLETED	Prospective Study Evaluating the Effect of Repository Corticotropin in the Treatment of Various Nephrotic Syndromes
NCT01028287	PHASE4	COMPLETED	Adrenocorticotropic Hormone (ACTH) Treatment of Nephrotic Range Proteinuria in Diabetic Nephropathy (NRDN)
NCT01162005	PHASE4	COMPLETED	Therapeutic Effect of Tacrolimus on Primary Nephrotic Syndrome in Children
NCT01895894	PHASE4	COMPLETED	Mycophenolate Mofetil in Pediatric Steroid Dependent Nephrotic Syndrome
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