SLC60A2

Summary

SLC60A2 (solute carrier family 60 member 2, HGNC:21053) is a protein-coding gene on chromosome 6q21, encoding Solute carrier family 60 member 1 (Q5TF39). Low-affinity Na(+)-dependent glucose symporter with a Na(+) to glucose coupling ratio of 1:1.

Predicted to enable symporter activity. Predicted to be involved in sodium ion transport and transmembrane transport. Predicted to be located in apical plasma membrane.

Source: NCBI Gene 91749 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_153369

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21053
Approved symbol	SLC60A2
Name	solute carrier family 60 member 2
Location	6q21
Locus type	gene with protein product
Status	Approved
Aliases	MGC33953
Ensembl gene	ENSG00000173214
Ensembl biotype	protein_coding
OMIM	617331
Entrez	91749

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 10 protein_coding_CDS_not_defined, 5 protein_coding, 3 nonsense_mediated_decay

ENST00000368847, ENST00000444259, ENST00000653951, ENST00000654539, ENST00000658925, ENST00000660710, ENST00000666581, ENST00000671876, ENST00000671883, ENST00000672191, ENST00000672303, ENST00000672494, ENST00000672554, ENST00000672750, ENST00000673024, ENST00000673164, ENST00000673245, ENST00000673446

RefSeq mRNA: 1 — MANE Select: NM_153369 NM_153369

CCDS: CCDS5090

Canonical transcript exons

ENST00000671876 — 4 exons

Exon	Start	End
ENSE00001218316	111263830	111263946
ENSE00001218322	111262257	111262425
ENSE00003888971	111265876	111280005
ENSE00003889710	111259339	111259727

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 93.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.5281 / max 256.6770, expressed in 1771 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
69284	9.7823	1758
69285	1.5251	661
69286	0.1346	43
69289	0.0465	11
69288	0.0336	11
69287	0.0061	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
renal medulla	UBERON:0000362	93.74	gold quality
kidney epithelium	UBERON:0004819	92.77	silver quality
buccal mucosa cell	CL:0002336	91.41	gold quality
nipple	UBERON:0002030	89.06	gold quality
jejunal mucosa	UBERON:0000399	88.74	gold quality
colonic epithelium	UBERON:0000397	87.30	gold quality
adrenal tissue	UBERON:0018303	87.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.42	gold quality
pylorus	UBERON:0001166	85.26	gold quality
sperm	CL:0000019	84.55	gold quality
calcaneal tendon	UBERON:0003701	84.48	gold quality
placenta	UBERON:0001987	84.33	gold quality
thymus	UBERON:0002370	84.20	gold quality
cardia of stomach	UBERON:0001162	83.84	gold quality
jejunum	UBERON:0002115	83.28	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.21	gold quality
sural nerve	UBERON:0015488	82.80	gold quality
cortex of kidney	UBERON:0001225	82.21	gold quality
bronchial epithelial cell	CL:0002328	82.20	gold quality
bronchus	UBERON:0002185	82.19	gold quality
corpus callosum	UBERON:0002336	81.83	gold quality
superior surface of tongue	UBERON:0007371	81.71	gold quality
pancreatic ductal cell	CL:0002079	81.70	silver quality
duodenum	UBERON:0002114	81.53	gold quality
kidney	UBERON:0002113	81.44	gold quality
trachea	UBERON:0003126	80.73	gold quality
right uterine tube	UBERON:0001302	80.49	gold quality
trabecular bone tissue	UBERON:0002483	80.32	gold quality
mammalian vulva	UBERON:0000997	80.13	gold quality
endometrium	UBERON:0001295	80.01	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 10.

Experiment	Marker?	Max mean expression
E-MTAB-5061	yes	3144.80
E-MTAB-8894	yes	1410.05
E-MTAB-6678	yes	437.53
E-HCAD-4	yes	81.53
E-CURD-119	yes	46.14
E-MTAB-9467	yes	42.92
E-HCAD-9	yes	16.74
E-CURD-88	yes	15.43
E-MTAB-8142	yes	15.05
E-MTAB-6701	yes	11.32
E-HCAD-8	no	24.92
E-CURD-46	no	5.84
E-ANND-3	no	5.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

95 targeting SLC60A2, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
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-548C-3P	99.99	74.01	7587
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	mfsd4b	ENSDARG00000079571
mus_musculus	Mfsd4b1	ENSMUSG00000038522
mus_musculus	Mfsd4b5	ENSMUSG00000038528
mus_musculus	Mfsd4b4	ENSMUSG00000096687
rattus_norvegicus	Mfsd4b2l1	ENSRNOG00000000589
rattus_norvegicus	Naglt1	ENSRNOG00000000590
rattus_norvegicus	Mfsd4b1	ENSRNOG00000024543
rattus_norvegicus	Mfsd4b2	ENSRNOG00000042918
rattus_norvegicus	Mfsd4b2l2	ENSRNOG00000050425

Paralogs (1): MFSD4A (ENSG00000174514)

Protein

Protein identifiers

Solute carrier family 60 member 1 — Q5TF39 (reviewed: Q5TF39)

Alternative names: Major facilitator superfamily domain-containing protein 4B, Sodium-dependent glucose transporter 1

All UniProt accessions (5): Q5TF39, A0A5F9ZH20, A0A5F9ZH60, A0A5F9ZH84, A0A5K1VW69

UniProt curated annotations — full annotation on UniProt →

Function. Low-affinity Na(+)-dependent glucose symporter with a Na(+) to glucose coupling ratio of 1:1. Potential channels for urea in the inner medulla of kidney.

Subcellular location. Apical cell membrane.

Similarity. Belongs to the SLC60A transporter family.

RefSeq proteins (1): NP_699200* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011701	MFS	Family
IPR036259	MFS_trans_sf	Homologous_superfamily

Pfam: PF07690

Catalyzed reactions (Rhea), 1 shown:

• D-glucose(out) + Na(+)(out) = D-glucose(in) + Na(+)(in) (RHEA:70571)

UniProt features (17 total): transmembrane region 12, compositionally biased region 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TF39-F1	78.02	0.51

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-189200	Cellular hexose transport
R-HSA-382551	Transport of small molecules
R-HSA-425407	SLC-mediated transmembrane transport

MSigDB gene sets: 115 (showing top): GOBP_CARBOHYDRATE_TRANSPORT, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MONOATOMIC_CATION_TRANSPORT, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, LIAO_METASTASIS, GOCC_APICAL_PLASMA_MEMBRANE, GOBP_IMPORT_INTO_CELL, GOBP_TRANSMEMBRANE_TRANSPORT, GOBP_SODIUM_ION_TRANSPORT, GOCC_CELL_PROJECTION_MEMBRANE, GOCC_APICAL_PART_OF_CELL, GOCC_CLUSTER_OF_ACTIN_BASED_CELL_PROJECTIONS, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_PLASMA_MEMBRANE_REGION

GO Biological Process (4): D-glucose import across plasma membrane (GO:0098708), monoatomic ion transport (GO:0006811), sodium ion transport (GO:0006814), transmembrane transport (GO:0055085)

GO Molecular Function (4): D-glucose:sodium symporter activity (GO:0005412), protein binding (GO:0005515), symporter activity (GO:0015293), transmembrane transporter activity (GO:0022857)

GO Cellular Component (4): brush border membrane (GO:0031526), plasma membrane (GO:0005886), membrane (GO:0016020), apical plasma membrane (GO:0016324)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
SLC-mediated transmembrane transport	1
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
hexose import across plasma membrane	1
D-glucose transmembrane transport	1
metal ion transport	1
cellular process	1
carbohydrate:monoatomic cation symporter activity	1
solute:sodium symporter activity	1
D-glucose transmembrane transporter activity	1
binding	1
secondary active transmembrane transporter activity	1
transporter activity	1
transmembrane transport	1
brush border	1
apical plasma membrane	1
cell projection membrane	1
membrane	1
cell periphery	1
cellular anatomical structure	1
apical part of cell	1
plasma membrane region	1

Protein interactions and networks

STRING

802 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC60A2	SLC5A1	P13866	791
SLC60A2	SLC2A2	P11168	587
SLC60A2	SLC67A2	Q8NBP5	519
SLC60A2	SLC15A1	P46059	510
SLC60A2	BASP1	P80723	498
SLC60A2	LCT	P09848	480
SLC60A2	SLC2A5	P22732	454
SLC60A2	SLC5A10	A0PJK1	425
SLC60A2	AMY2A	P04746	409
SLC60A2	MGAM	O43451	389
SLC60A2	SLC2A8	Q9NY64	377
SLC60A2	GTF3C6	Q969F1	370
SLC60A2	TAS1R2	Q8TE23	365
SLC60A2	SI	P14410	364
SLC60A2	SLC5A9	Q2M3M2	363

IntAct

34 interactions, top by confidence:

A	B	Type	Score
PRKAG1	PRKAB2	psi-mi:“MI:0914”(association)	0.940
EIF2B2	SLC27A2	psi-mi:“MI:0914”(association)	0.640
MFSD4B	DCBLD2	psi-mi:“MI:0915”(physical association)	0.560
CYB5B	MFSD4B	psi-mi:“MI:0915”(physical association)	0.560
MFSD4B	VSTM1	psi-mi:“MI:0915”(physical association)	0.560
MFSD4B	MFSD6	psi-mi:“MI:0915”(physical association)	0.560
DHRS9	MFSD4B	psi-mi:“MI:0914”(association)	0.530
ATP6V0D1		psi-mi:“MI:0914”(association)	0.350
	TXNDC9	psi-mi:“MI:0914”(association)	0.350
GNAI2	GNG7	psi-mi:“MI:0914”(association)	0.350
DPH6	ATP2B2	psi-mi:“MI:0914”(association)	0.350
DHRS9	ATP2B2	psi-mi:“MI:0914”(association)	0.350
CRYL1	MYO9A	psi-mi:“MI:0914”(association)	0.350
GPR12	TLCD2	psi-mi:“MI:0914”(association)	0.350
TUBA3C	TXNDC9	psi-mi:“MI:0914”(association)	0.350
SPAG6	MT-ND1	psi-mi:“MI:0914”(association)	0.350
C1orf74	HCK	psi-mi:“MI:0914”(association)	0.350
ART3	NCF1	psi-mi:“MI:0914”(association)	0.350
KYNU	ACTA2	psi-mi:“MI:0914”(association)	0.350
MFSD4B	XPOT	psi-mi:“MI:0914”(association)	0.350
MFSD4B	DYNC2H1	psi-mi:“MI:0915”(physical association)	0.000
CYB5B	MFSD4B	psi-mi:“MI:0915”(physical association)	0.000
VSTM1	MFSD4B	psi-mi:“MI:0915”(physical association)	0.000
MFSD6	MFSD4B	psi-mi:“MI:0915”(physical association)	0.000
DCBLD2	MFSD4B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (60): KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), KIAA1919 (Affinity Capture-MS), DYNC2H1 (Affinity Capture-MS), KIAA1919 (Affinity Capture-RNA), KIAA1919 (Two-hybrid)

ESM2 similar proteins: A1L272, A4FUY9, A5D7C9, A5PN43, A9JSP6, B5DFH9, B9EJG8, D3ZEH5, E2RFJ3, O19133, O70578, P35575, P51811, P97707, Q19KA1, Q28BP2, Q28CV2, Q29RU6, Q49LS5, Q569T7, Q5F383, Q5GH61, Q5TF39, Q5ZI05, Q5ZKY0, Q640L2, Q6GPL4, Q6GQE1, Q6PF45, Q7SYC7, Q80UF9, Q86TG1, Q86X19, Q8BMD6, Q8C8S3, Q8CIF6, Q8CJ61, Q8IZ96, Q8NBJ9, Q8R000

Diamond homologs: A4QN56, Q569T7, Q5TF39, Q80T22, Q8VCV9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

6473 predictions. Top by Δscore:

Variant	Effect	Δscore
6:111262251:TTTTA:T	acceptor_loss	1.0000
6:111262252:TTTA:T	acceptor_loss	1.0000
6:111262253:TTA:T	acceptor_loss	1.0000
6:111262255:A:AG	acceptor_gain	1.0000
6:111262255:AG:A	acceptor_gain	1.0000
6:111262255:AGG:A	acceptor_gain	1.0000
6:111262255:AGGG:A	acceptor_loss	1.0000
6:111262256:G:GG	acceptor_gain	1.0000
6:111262256:GG:G	acceptor_gain	1.0000
6:111262256:GGG:G	acceptor_gain	1.0000
6:111262421:TTTGG:T	donor_gain	1.0000
6:111262422:TTGGG:T	donor_loss	1.0000
6:111262423:TGGGT:T	donor_loss	1.0000
6:111262424:GG:G	donor_gain	1.0000
6:111262424:GGGTA:G	donor_loss	1.0000
6:111262425:GG:G	donor_gain	1.0000
6:111262425:GGT:G	donor_loss	1.0000
6:111262426:G:GG	donor_gain	1.0000
6:111262426:GTAA:G	donor_loss	1.0000
6:111262427:TAA:T	donor_loss	1.0000
6:111265370:AAT:A	acceptor_gain	1.0000
6:111265370:AATG:A	acceptor_gain	1.0000
6:111265372:T:TA	acceptor_gain	1.0000
6:111265373:G:A	acceptor_gain	1.0000
6:111310095:TTTTC:T	acceptor_gain	1.0000
6:111310100:C:CC	acceptor_gain	1.0000
6:111310111:C:CT	acceptor_gain	1.0000
6:111310112:A:T	acceptor_gain	1.0000
6:111311261:T:C	acceptor_gain	1.0000
6:111313346:CCTTA:C	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000236940 (6:111264585 G>A), RS1000344645 (6:111258067 T>A), RS1000862400 (6:111257855 G>A), RS1000915788 (6:111262221 A>G), RS1000916529 (6:111268661 C>G,T), RS1000940906 (6:111272734 A>G), RS1001036896 (6:111268369 A>T), RS1001263172 (6:111261854 A>G), RS1001316823 (6:111265645 T>C), RS1001472328 (6:111259087 G>A), RS1001480853 (6:111264961 C>T), RS1001500659 (6:111274704 A>G), RS1001554838 (6:111279229 T>C), RS1001604886 (6:111278063 C>G), RS1001711111 (6:111270924 A>G)

Disease associations

OMIM: gene MIM:617331 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002740_41	Inflammatory skin disease	1.000000e-16
GCST004131_98	Inflammatory bowel disease	4.000000e-10
GCST004133_60	Ulcerative colitis	6.000000e-10
GCST90002403_170	Red blood cell count	5.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004305	erythrocyte count

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 — SLC60 Glucose transporters

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	2
trichostatin A	affects expression	1
mesotrione	increases abundance, affects methylation	1
bisphenol S	affects cotreatment, decreases methylation	1
(+)-JQ1 compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Caffeine	increases phosphorylation	1
Herbicides	affects methylation, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	decreases expression	1
Acrylamide	decreases expression	1
Particulate Matter	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_D4GN	HCT116-MFSD4B-KO-c2	Cancer cell line	Male
CVCL_D4GP	HCT116-MFSD4B-KO-c3	Cancer cell line	Male

Clinical trials (associated diseases)

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