SLC35E2B

Summary

SLC35E2B (solute carrier family 35 member E2B, HGNC:33941) is a protein-coding gene on chromosome 1p36.33, encoding Solute carrier family 35 member E2B (P0CK96). Putative transporter.

Predicted to enable antiporter activity. Predicted to be involved in transmembrane transport. Predicted to act upstream of or within blastocyst hatching. Predicted to be located in membrane. Predicted to be active in Golgi apparatus.

Source: NCBI Gene 728661 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_001290264

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33941
Approved symbol	SLC35E2B
Name	solute carrier family 35 member E2B
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000189339
Ensembl biotype	protein_coding
OMIM	619315
Entrez	728661

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 2 retained_intron

ENST00000480991, ENST00000481276, ENST00000611123, ENST00000614300, ENST00000617444, ENST00000904336, ENST00000904337, ENST00000904338, ENST00000904339, ENST00000904340, ENST00000911898, ENST00000911899, ENST00000911900, ENST00000911901, ENST00000956985

RefSeq mRNA: 2 — MANE Select: NM_001290264 NM_001110781, NM_001290264

CCDS: CCDS44041

Canonical transcript exons

ENST00000617444 — 10 exons

Exon	Start	End
ENSE00003716052	1675463	1675590
ENSE00003719360	1692449	1692795
ENSE00003719420	1676378	1676846
ENSE00003726934	1671509	1671629
ENSE00003728071	1676064	1676199
ENSE00003730248	1661478	1666019
ENSE00003732837	1690976	1691393
ENSE00003732855	1668327	1668472
ENSE00003739608	1669664	1669736
ENSE00003739651	1670098	1670151

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 98.62.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7776 / max 7.5722, expressed in 541 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
201317	0.4358	232
9819	0.3418	200

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibia	UBERON:0000979	98.62	gold quality
thymus	UBERON:0002370	98.35	gold quality
postcentral gyrus	UBERON:0002581	98.18	gold quality
parietal lobe	UBERON:0001872	97.69	gold quality
Brodmann (1909) area 10	UBERON:0013541	97.51	gold quality
cerebellar vermis	UBERON:0004720	97.48	gold quality
Brodmann (1909) area 46	UBERON:0006483	97.48	gold quality
middle temporal gyrus	UBERON:0002771	97.22	gold quality
germinal epithelium of ovary	UBERON:0001304	97.19	gold quality
entorhinal cortex	UBERON:0002728	97.16	gold quality
paraflocculus	UBERON:0005351	97.15	gold quality
cortical plate	UBERON:0005343	97.14	gold quality
parietal pleura	UBERON:0002400	97.03	gold quality
superior frontal gyrus	UBERON:0002661	97.03	gold quality
cardia of stomach	UBERON:0001162	97.01	gold quality
ileal mucosa	UBERON:0000331	97.00	gold quality
seminal vesicle	UBERON:0000998	96.91	gold quality
superficial temporal artery	UBERON:0001614	96.91	gold quality
orbitofrontal cortex	UBERON:0004167	96.87	gold quality
renal medulla	UBERON:0000362	96.84	gold quality
inferior olivary complex	UBERON:0002127	96.73	gold quality
epithelium of mammary gland	UBERON:0003244	96.73	gold quality
medial globus pallidus	UBERON:0002477	96.72	gold quality
jejunal mucosa	UBERON:0000399	96.71	gold quality
pleura	UBERON:0000977	96.66	gold quality
pylorus	UBERON:0001166	96.63	gold quality
mammary duct	UBERON:0001765	96.63	gold quality
skin of hip	UBERON:0001554	96.59	gold quality
visceral pleura	UBERON:0002401	96.59	gold quality
bronchial epithelial cell	CL:0002328	96.50	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.71
E-CURD-112	no	3.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

150 targeting SLC35E2B, 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-4481	100.00	66.42	1669
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-8075	99.97	67.20	962

Literature-anchored findings (GeneRIF, showing 1)

• Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe. (PMID:33711669)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	SLC35E2B	ENSDARG00000109717
mus_musculus	Slc35e2	ENSMUSG00000042202
rattus_norvegicus	Slc35e2	ENSRNOG00000062404

Paralogs (9): SLC35C2 (ENSG00000080189), SLC35E4 (ENSG00000100036), SLC35D1 (ENSG00000116704), SLC35E1 (ENSG00000127526), SLC35D2 (ENSG00000130958), TMEM241 (ENSG00000134490), SLC35E3 (ENSG00000175782), SLC35C1 (ENSG00000181830), SLC35D3 (ENSG00000182747)

Protein

Protein identifiers

Solute carrier family 35 member E2B — P0CK96 (reviewed: P0CK96)

All UniProt accessions (2): A0A087WUK8, P0CK96

UniProt curated annotations — full annotation on UniProt →

Function. Putative transporter.

Subcellular location. Membrane.

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

RefSeq proteins (2): NP_001104251, NP_001277193* (*=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 (15 total): transmembrane region 10, region of interest 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CK96-F1	73.85	0.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): SCHLOSSER_SERUM_RESPONSE_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, HOEBEKE_LYMPHOID_STEM_CELL_UP, GOBP_TRANSMEMBRANE_TRANSPORT, GOMF_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_SECONDARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, BROWNE_HCMV_INFECTION_16HR_DN, GOMF_TRANSPORTER_ACTIVITY, chr1p36, LUI_THYROID_CANCER_CLUSTER_1, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, GUCY1B1_TARGET_GENES, SETD7_TARGET_GENES, SKIL_TARGET_GENES, ZNF322_TARGET_GENES

GO Biological Process (2): blastocyst hatching (GO:0001835), transmembrane transport (GO:0055085)

GO Molecular Function (1): antiporter activity (GO:0015297)

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

GO top-level categories

Rollup of top GO terms by namespace:

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

Protein interactions and networks

STRING

638 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC35E2B	SLC35G4	P0C7Q5	544
SLC35E2B	TMEM250	H0YL14	505
SLC35E2B	ZNF850	A8MQ14	480
SLC35E2B	PRAMEF18	Q5VWM3	474
SLC35E2B	SLC35F6	Q8N357	454
SLC35E2B	PRAMEF7	Q5VXH5	447
SLC35E2B	SLC35G1	Q2M3R5	439
SLC35E2B	SLC22A25	Q6T423	429
SLC35E2B	SLC35G3	Q8N808	425
SLC35E2B	ZNF490	Q9ULM2	419
SLC35E2B	NOL9	Q5SY16	415
SLC35E2B	SLC35C1	Q96A29	399
SLC35E2B	SLC35G2	Q8TBE7	394
SLC35E2B	PLCXD1	Q9NUJ7	392
SLC35E2B	GNL3L	Q9NVN8	390

IntAct

5 interactions, top by confidence:

A	B	Type	Score
P		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
ICAM2	RAB29	psi-mi:“MI:0914”(association)	0.350
SLC35E2B	ERLIN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (13): SLC35E2B (Affinity Capture-MS), SLC35E2B (Affinity Capture-RNA), SLC35E2B (Affinity Capture-RNA), SLC35E2B (Two-hybrid), AASS (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), ERLIN1 (Affinity Capture-MS), ERLIN2 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), RAB18 (Affinity Capture-MS), RAB6A (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC35E2B (Affinity Capture-RNA)

ESM2 similar proteins: A1A5C7, A6H7A0, B0BMW8, B0CM95, B0KWE9, B1MTH4, B2KI79, O43688, O62772, O75147, P0CK96, P35438, P35439, P52875, P57791, Q05586, Q28D01, Q2KJ29, Q3KNV8, Q3SZQ2, Q3UHH2, Q4L208, Q4V899, Q5R1P0, Q5R890, Q5SP67, Q5ZJ75, Q7TPB4, Q86YN1, Q8BTQ0, Q8C6G8, Q8C811, Q8R4D1, Q8VDI9, Q8VE98, Q90812, Q9BWV1, Q9D9E0, Q9H6U8, Q9H7D7

Diamond homologs: O94695, P0C6B1, P0CK96, P52178, Q5VQL3, Q69VR7, Q84QU8, Q8C811, Q8CD26, Q94B38, Q96K37, Q9LF61, Q9M5A9, Q9VR50, P0CK97, P21727, P29463, P49131, P49132, P49133, P52177, Q8H0T6, Q8RXN3, O81514, P11869, Q9FTT3, Q9ZSR7, P0DQY4, Q5XF09, Q6DBP3, Q9LDH3

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	57
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2626 predictions. Top by Δscore:

Variant	Effect	Δscore
1:1668322:CTCA:C	donor_loss	1.0000
1:1668324:CAC:C	donor_loss	1.0000
1:1668468:ACGTC:A	acceptor_gain	1.0000
1:1668469:CGTC:C	acceptor_gain	1.0000
1:1668469:CGTCC:C	acceptor_gain	1.0000
1:1668470:GTC:G	acceptor_gain	1.0000
1:1668471:TC:T	acceptor_gain	1.0000
1:1668471:TCC:T	acceptor_loss	1.0000
1:1668472:CC:C	acceptor_gain	1.0000
1:1668473:C:CA	acceptor_loss	1.0000
1:1668473:C:CC	acceptor_gain	1.0000
1:1668475:A:AC	acceptor_gain	1.0000
1:1668475:A:C	acceptor_gain	1.0000
1:1668477:G:C	acceptor_gain	1.0000
1:1668477:G:GC	acceptor_gain	1.0000
1:1668481:C:CT	acceptor_gain	1.0000
1:1668482:A:T	acceptor_gain	1.0000
1:1675586:CAAAC:C	acceptor_gain	1.0000
1:1675589:ACCTA:A	acceptor_loss	1.0000
1:1675591:CTA:C	acceptor_loss	1.0000
1:1676372:GCCTA:G	donor_loss	1.0000
1:1676375:TACCT:T	donor_loss	1.0000
1:1676376:AC:A	donor_loss	1.0000
1:1665774:T:TA	donor_gain	0.9900
1:1668325:A:AC	donor_gain	0.9900
1:1668326:C:CC	donor_gain	0.9900
1:1668473:C:T	acceptor_gain	0.9900
1:1670096:A:AC	donor_gain	0.9900
1:1670097:C:CC	donor_gain	0.9900
1:1670148:CAAA:C	acceptor_gain	0.9900

AlphaMissense

2623 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:1665912:C:T	G363E	0.998
1:1665913:C:G	G363R	0.998
1:1665913:C:T	G363R	0.998
1:1666017:A:T	V328D	0.998
1:1670130:T:A	K243N	0.998
1:1670130:T:G	K243N	0.998
1:1670131:T:A	K243I	0.998
1:1671608:A:G	L203P	0.998
1:1671608:A:T	L203H	0.998
1:1675518:G:C	S177R	0.998
1:1675518:G:T	S177R	0.998
1:1675520:T:G	S177R	0.998
1:1665933:C:T	G356D	0.997
1:1666001:T:A	K333N	0.997
1:1666001:T:G	K333N	0.997
1:1668357:A:G	L317P	0.997
1:1670142:A:C	N239K	0.997
1:1670142:A:T	N239K	0.997
1:1670151:A:C	C236W	0.997
1:1671590:C:T	G209E	0.997
1:1671591:C:G	G209R	0.997
1:1671591:C:T	G209R	0.997
1:1671599:A:T	V206D	0.997
1:1675510:G:C	P180R	0.997
1:1675510:G:T	P180H	0.997
1:1676456:A:G	W82R	0.997
1:1676456:A:T	W82R	0.997
1:1665934:C:G	G356R	0.996
1:1665977:G:C	S341R	0.996
1:1665977:G:T	S341R	0.996

dbSNP variants (sampled 300 via entrez): RS1000238116 (1:1665707 T>C), RS1000238748 (1:1674140 A>G), RS1000247735 (1:1670546 C>T), RS1000453965 (1:1674249 G>A,T), RS1000492129 (1:1687188 GCA>G,GCACA,GCACACA), RS1000505557 (1:1685510 G>A), RS1000543016 (1:1682931 G>A), RS1000737760 (1:1693852 G>A,C), RS1000852177 (1:1673117 C>G), RS1000931051 (1:1678361 G>A), RS1000983408 (1:1678148 C>T), RS1001089801 (1:1694116 C>A,G,T), RS1001150162 (1:1693557 C>G), RS1001216536 (1:1665630 G>C), RS1001257187 (1:1669490 A>G)

Disease associations

OMIM: gene MIM:619315 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005951_34	Body mass index	3.000000e-08
GCST010988_518	Adult body size	2.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases methylation	5
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	increases expression	1
sodium arsenite	decreases expression, increases abundance, affects cotreatment	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Cadmium	increases expression, increases abundance	1
Dexamethasone	decreases expression, affects cotreatment	1
Gallic Acid	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases abundance, increases expression	1
Okadaic Acid	decreases expression	1

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2G2	Abcam HeLa SLC35E2B KO	Cancer cell line	Female
CVCL_D4MD	HCT116-SLC35E2B-KO-c15	Cancer cell line	Male
CVCL_D4ME	HCT116-SLC35E2B-KO-c8	Cancer cell line	Male
CVCL_TN21	HAP1 SLC35E2B (-) 1	Cancer cell line	Male
CVCL_TN22	HAP1 SLC35E2B (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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