SLC35E1

Summary

SLC35E1 (solute carrier family 35 member E1, HGNC:20803) is a protein-coding gene on chromosome 19p13.11, encoding Solute carrier family 35 member E1 (Q96K37). Putative transporter.

Predicted to enable antiporter activity. Predicted to be involved in transmembrane transport. Located in Golgi apparatus.

Source: NCBI Gene 79939 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 53 total
• Druggable target: yes
• MANE Select transcript: NM_024881

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20803
Approved symbol	SLC35E1
Name	solute carrier family 35 member E1
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14251
Ensembl gene	ENSG00000127526
Ensembl biotype	protein_coding
OMIM	620337
Entrez	79939

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 6 protein_coding, 5 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000409648, ENST00000421082, ENST00000436553, ENST00000469055, ENST00000470077, ENST00000488894, ENST00000593812, ENST00000595753, ENST00000596387, ENST00000600356, ENST00000652421, ENST00000929426, ENST00000929427, ENST00000960529

RefSeq mRNA: 1 — MANE Select: NM_024881 NM_024881

CCDS: CCDS12346

Canonical transcript exons

ENST00000595753 — 6 exons

Exon	Start	End
ENSE00002273520	16571944	16572415
ENSE00003029375	16549837	16553909
ENSE00003489403	16568032	16568169
ENSE00003630411	16555152	16555397
ENSE00003636706	16566532	16566657
ENSE00003637076	16571512	16571582

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 99.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.4160 / max 70.3663, expressed in 1802 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179816	17.9688	1797
179815	0.4472	232

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
renal medulla	UBERON:0000362	99.77	gold quality
cardia of stomach	UBERON:0001162	99.75	gold quality
nipple	UBERON:0002030	99.70	gold quality
pylorus	UBERON:0001166	99.69	gold quality
ventral tegmental area	UBERON:0002691	99.66	gold quality
trigeminal ganglion	UBERON:0001675	99.65	gold quality
superior surface of tongue	UBERON:0007371	99.61	gold quality
dorsal root ganglion	UBERON:0000044	99.55	gold quality
superior vestibular nucleus	UBERON:0007227	99.55	gold quality
inferior vagus X ganglion	UBERON:0005363	99.53	gold quality
trachea	UBERON:0003126	99.50	gold quality
endothelial cell	CL:0000115	99.48	gold quality
subthalamic nucleus	UBERON:0001906	99.44	gold quality
pericardium	UBERON:0002407	99.39	gold quality
visceral pleura	UBERON:0002401	99.36	gold quality
medulla oblongata	UBERON:0001896	99.31	gold quality
buccal mucosa cell	CL:0002336	99.30	gold quality
pharyngeal mucosa	UBERON:0000355	99.28	gold quality
dorsal plus ventral thalamus	UBERON:0001897	99.28	gold quality
pons	UBERON:0000988	99.26	gold quality
saphenous vein	UBERON:0007318	99.24	gold quality
sperm	CL:0000019	99.23	gold quality
male germ cell	CL:0000015	99.22	gold quality
lateral globus pallidus	UBERON:0002476	99.21	gold quality
superficial temporal artery	UBERON:0001614	99.13	gold quality
urethra	UBERON:0000057	99.11	gold quality
pleura	UBERON:0000977	99.09	gold quality
mucosa of paranasal sinus	UBERON:0005030	99.08	gold quality
body of tongue	UBERON:0011876	99.06	gold quality
periodontal ligament	UBERON:0008266	99.05	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.45
E-MTAB-7606	no	472.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

128 targeting SLC35E1, 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-LET-7F-1-3P	100.00	74.02	3928
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-181D-5P	99.99	73.04	2997
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-371B-5P	99.99	75.34	4759
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-150-5P	99.99	66.69	1976
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-570-3P	99.96	72.41	4910

Literature-anchored findings (GeneRIF, showing 1)

• Role of the Orphan Transporter SLC35E1 in the Nuclear Egress of Herpes Simplex Virus 1. (PMID:35475666)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc35e1	ENSDARG00000011945
mus_musculus	Slc35e1	ENSMUSG00000019731
rattus_norvegicus	Slc35e1	ENSRNOG00000012287
drosophila_melanogaster	CG14621	FBGN0031183

Paralogs (9): SLC35C2 (ENSG00000080189), SLC35E4 (ENSG00000100036), SLC35D1 (ENSG00000116704), SLC35D2 (ENSG00000130958), TMEM241 (ENSG00000134490), SLC35E3 (ENSG00000175782), SLC35C1 (ENSG00000181830), SLC35D3 (ENSG00000182747), SLC35E2B (ENSG00000189339)

Protein

Protein identifiers

Solute carrier family 35 member E1 — Q96K37 (reviewed: Q96K37)

All UniProt accessions (4): Q96K37, A0A0A0MSG4, C9JK45, H7C1I0

UniProt curated annotations — full annotation on UniProt →

Function. Putative transporter.

Subcellular location. Membrane.

Similarity. Belongs to the TPT transporter family. SLC35E subfamily.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96K37-1	1	yes
Q96K37-2	2
Q96K37-3	3

RefSeq proteins (1): NP_079157* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004853	Sugar_P_trans_dom	Domain
IPR037185	EmrE-like	Homologous_superfamily
IPR050186	TPT_transporter	Family

Pfam: PF03151

UniProt features (17 total): transmembrane region 9, splice variant 4, sequence conflict 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96K37-F1	75.05	0.41

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 363

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): PEREZ_TP63_TARGETS, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, TGCTGAY_UNKNOWN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, WHN_B, GOBP_TRANSMEMBRANE_TRANSPORT, DR3_Q4, CP2_01, chr19p13, NUYTTEN_NIPP1_TARGETS_DN, GOMF_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, LIU_COMMON_CANCER_GENES, GOMF_SECONDARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_TRANSPORTER_ACTIVITY, TIEN_INTESTINE_PROBIOTICS_24HR_DN

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

GO Molecular Function (2): antiporter activity (GO:0015297), protein binding (GO:0005515)

GO Cellular Component (2): Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
secondary active transmembrane transporter activity	1
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

912 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC35E1	SLC35D1	Q9NTN3	695
SLC35E1	SLC35H1	Q9NQQ7	688
SLC35E1	SLC35C1	Q96A29	687
SLC35E1	SLC35A1	P78382	619
SLC35E1	SLC35B4	Q969S0	607
SLC35E1	SLC35F1	Q5T1Q4	584
SLC35E1	SLC35G1	Q2M3R5	573
SLC35E1	SLC35D3	Q5M8T2	565
SLC35E1	SLC35B1	P78383	550
SLC35E1	SLC35A5	Q9BS91	548
SLC35E1	SLC35B2	Q8TB61	540
SLC35E1	SLC35A4	Q96G79	536
SLC35E1	NR2C2AP	Q86WQ0	525
SLC35E1	SLC35D2	Q76EJ3	513
SLC35E1	SLC35B3	Q9H1N7	513

IntAct

99 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
IFT27	IFT56	psi-mi:“MI:0914”(association)	0.690
PKN3	ARHGAP10	psi-mi:“MI:0914”(association)	0.680
MPP1	SLC35E1	psi-mi:“MI:0915”(physical association)	0.560
SLC35E1	FTHL17	psi-mi:“MI:0915”(physical association)	0.560
GRK7	HSP90AA1	psi-mi:“MI:0914”(association)	0.530
ARMC6	SLC27A2	psi-mi:“MI:0914”(association)	0.530
SLC6A8	ILVBL	psi-mi:“MI:0914”(association)	0.530
IFT52	IFT56	psi-mi:“MI:0914”(association)	0.510
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
Rab5c		psi-mi:“MI:0914”(association)	0.350
Magoh	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
GJB2	SNX3	psi-mi:“MI:0914”(association)	0.350
Cct3	PFDN1	psi-mi:“MI:0914”(association)	0.350
Kcnk1	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
RAB5C	GCA	psi-mi:“MI:0914”(association)	0.350
Atp2a2	ESYT2	psi-mi:“MI:0914”(association)	0.350
Smn1	CLNS1A	psi-mi:“MI:0914”(association)	0.350
Csnk1d	WWP2	psi-mi:“MI:0914”(association)	0.350
TENT5A	GOLGA8R	psi-mi:“MI:0914”(association)	0.350
KIF2A	GNS	psi-mi:“MI:0914”(association)	0.350
Sec24c	SEC31A	psi-mi:“MI:0914”(association)	0.350
ARMC6		psi-mi:“MI:0914”(association)	0.350
Tmed2		psi-mi:“MI:0914”(association)	0.350
Uso1	SLC30A6	psi-mi:“MI:0914”(association)	0.350
MBOAT1	DERL1	psi-mi:“MI:0914”(association)	0.350

BioGRID (146): SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS), SLC35E1 (Affinity Capture-MS)

ESM2 similar proteins: A6QL92, A8MRY9, B0BMY1, B8A7Q8, P0C6B1, P43007, P57057, Q04671, Q08D99, Q08DX7, Q10PI5, Q12887, Q1LZI2, Q2YDU8, Q3U481, Q4R794, Q5N855, Q5R460, Q5R6J3, Q5R9A1, Q69QJ7, Q6NM25, Q7RTT9, Q84L09, Q8CD26, Q8CFY5, Q8H184, Q8IY50, Q8K078, Q8R070, Q8R0G7, Q8R139, Q8R314, Q8RWW7, Q8TB61, Q8WV83, Q91WC7, Q91ZN5, Q96BD0, Q96HV5

Diamond homologs: O94695, P0C6B1, P22215, Q8CD26, Q96K37, Q9VR50, P0CK96, P52178, Q5VQL3, Q69VR7, Q84QU8, Q8C811, Q94B38, Q9LF61, Q9M5A9, P0CK97, P21727, P29463, P49131, P49132, P49133, P52177, Q8H0T6, Q8RXN3, P11869, Q9FTT3, Q9ZSR7, Q5XF09, Q6DBP3, Q9LDH3, O81514

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1099 predictions. Top by Δscore:

Variant	Effect	Δscore
19:16555146:TCTCA:T	donor_loss	1.0000
19:16555147:CTCAC:C	donor_loss	1.0000
19:16555148:TCAC:T	donor_loss	1.0000
19:16555148:TCACC:T	donor_loss	1.0000
19:16555149:CACCT:C	donor_loss	1.0000
19:16555150:AC:A	donor_gain	1.0000
19:16555151:CC:C	donor_gain	1.0000
19:16555393:TAGGT:T	acceptor_gain	1.0000
19:16555394:AGGT:A	acceptor_gain	1.0000
19:16555395:GGT:G	acceptor_gain	1.0000
19:16555395:GGTC:G	acceptor_loss	1.0000
19:16555396:GT:G	acceptor_gain	1.0000
19:16555396:GTC:G	acceptor_loss	1.0000
19:16555397:TCT:T	acceptor_loss	1.0000
19:16555398:C:CC	acceptor_gain	1.0000
19:16555398:C:CG	acceptor_loss	1.0000
19:16555398:C:T	acceptor_loss	1.0000
19:16555399:T:A	acceptor_loss	1.0000
19:16555408:C:CT	acceptor_gain	1.0000
19:16555408:C:T	acceptor_gain	1.0000
19:16555409:G:T	acceptor_gain	1.0000
19:16566529:CA:C	donor_loss	1.0000
19:16566530:A:AC	donor_gain	1.0000
19:16566531:C:CC	donor_gain	1.0000
19:16566531:C:CG	donor_loss	1.0000
19:16566531:C:CT	donor_loss	1.0000
19:16566653:AAGAC:A	acceptor_gain	1.0000
19:16566654:AGAC:A	acceptor_gain	1.0000
19:16566655:GAC:G	acceptor_gain	1.0000
19:16566656:AC:A	acceptor_gain	1.0000

AlphaMissense

2647 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:16555171:C:T	G328E	1.000
19:16555172:C:G	G328R	1.000
19:16555172:C:T	G328R	1.000
19:16555180:G:T	A325D	1.000
19:16555192:C:T	G321D	1.000
19:16555193:C:G	G321R	1.000
19:16555260:T:A	K298N	1.000
19:16555260:T:G	K298N	1.000
19:16555261:T:A	K298I	1.000
19:16555276:A:T	V293D	1.000
19:16555314:G:C	F280L	1.000
19:16555314:G:T	F280L	1.000
19:16555316:A:G	F280L	1.000
19:16568054:A:G	L203P	1.000
19:16568090:A:G	L191P	1.000
19:16568094:C:G	G190R	1.000
19:16568094:C:T	G190R	1.000
19:16568138:C:T	G175D	1.000
19:16568139:C:G	G175R	1.000
19:16568150:G:C	P171R	1.000
19:16568156:A:G	L169P	1.000
19:16568156:A:T	L169H	1.000
19:16571567:G:C	P146R	1.000
19:16571567:G:T	P146H	1.000
19:16571582:A:T	V141D	1.000
19:16571978:G:C	S129R	1.000
19:16571978:G:T	S129R	1.000
19:16571980:T:G	S129R	1.000
19:16572012:C:T	G118D	1.000
19:16572021:A:T	L115H	1.000

dbSNP variants (sampled 300 via entrez): RS1000004711 (19:16574019 C>G,T), RS1000093968 (19:16571540 A>G), RS1000141944 (19:16574272 T>A,G), RS1000257632 (19:16570946 A>C), RS1000286888 (19:16564772 T>C), RS1000361243 (19:16565215 CTTTT>C,CT,CTT,CTTT,CTTTTT,CTTTTTT), RS1000422425 (19:16565089 C>T), RS1000705337 (19:16572768 G>A), RS1000772901 (19:16571213 T>C,G), RS1000969936 (19:16560715 A>T), RS1000992322 (19:16572600 A>T), RS1001140849 (19:16554602 A>C,G), RS1001243220 (19:16560124 T>C), RS1001272780 (19:16560502 C>T), RS1001448997 (19:16565852 G>C,T)

Disease associations

OMIM: gene MIM:620337 | 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: yes

ChEMBL targets (1): CHEMBL6067429 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.36	Kd	4.39	nM	CHEMBL3752910
8.36	ED50	4.39	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149420: Binding affinity to human SLC35E1 incubated for 45 mins by Kinobead based pull down assay	kd	0.0044	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression	2
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	increases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
lead acetate	affects cotreatment, increases expression	1
zinc protoporphyrin	affects cotreatment, increases expression	1
sodium arsenite	increases expression	1
methacrylaldehyde	increases abundance, affects cotreatment, increases oxidation	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
abrine	decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	increases abundance, increases oxidation, affects cotreatment	1
Benzene	increases expression	1
Coumestrol	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Formaldehyde	increases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652462	Binding	Binding affinity to human SLC35E1 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4M9	HCT116-SLC35E1-KO-c4	Cancer cell line	Male
CVCL_D4MA	HCT116-SLC35E1-KO-c5	Cancer cell line	Male
CVCL_TN19	HAP1 SLC35E1 (-) 1	Cancer cell line	Male
CVCL_TN20	HAP1 SLC35E1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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