SLC60A1

Summary

SLC60A1 (solute carrier family 60 member 1, HGNC:25433) is a protein-coding gene on chromosome 1q32.1, encoding Solute carrier family 60 member 1 (Q8N468).

Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in membrane. Biomarker of cholangiocarcinoma.

Source: NCBI Gene 148808 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_181644

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25433
Approved symbol	SLC60A1
Name	solute carrier family 60 member 1
Location	1q32.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004
Ensembl gene	ENSG00000174514
Ensembl biotype	protein_coding
OMIM	620299
Entrez	148808

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000367147, ENST00000465651, ENST00000471425, ENST00000475956, ENST00000478555, ENST00000489709, ENST00000536357, ENST00000539267, ENST00000614644, ENST00000616173, ENST00000621216, ENST00000873626, ENST00000873627, ENST00000873628, ENST00000873629, ENST00000946000, ENST00000946001

RefSeq mRNA: 1 — MANE Select: NM_181644 NM_181644

CCDS: CCDS1455

Canonical transcript exons

ENST00000367147 — 10 exons

Exon	Start	End
ENSE00001443633	205569014	205569299
ENSE00003463438	205599131	205599251
ENSE00003530630	205584876	205584991
ENSE00003533355	205586034	205586207
ENSE00003538858	205597780	205597850
ENSE00003561214	205580661	205580921
ENSE00003597232	205579751	205579949
ENSE00003632526	205600406	205602918
ENSE00003674554	205583955	205584123
ENSE00003691264	205592140	205592287

Expression profiles

Bgee: expression breadth ubiquitous, 237 present calls, max score 99.36.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3698 / max 212.5266, expressed in 339 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
8048	0.8745	151
8049	0.5234	126
8054	0.4119	217
8045	0.2058	63
8047	0.1423	56
8052	0.0554	29
201899	0.0402	28
8046	0.0372	31
8050	0.0344	26
8051	0.0343	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
palpebral conjunctiva	UBERON:0001812	99.36	gold quality
renal medulla	UBERON:0000362	98.98	gold quality
middle temporal gyrus	UBERON:0002771	98.84	gold quality
kidney epithelium	UBERON:0004819	98.55	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.25	gold quality
nasal cavity epithelium	UBERON:0005384	98.05	gold quality
Brodmann (1909) area 23	UBERON:0013554	97.98	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.86	gold quality
endothelial cell	CL:0000115	97.22	gold quality
superior frontal gyrus	UBERON:0002661	96.00	gold quality
entorhinal cortex	UBERON:0002728	95.64	gold quality
postcentral gyrus	UBERON:0002581	95.49	gold quality
colonic mucosa	UBERON:0000317	95.48	gold quality
primary visual cortex	UBERON:0002436	95.21	gold quality
parietal lobe	UBERON:0001872	95.01	gold quality
occipital lobe	UBERON:0002021	94.32	gold quality
prefrontal cortex	UBERON:0000451	94.26	gold quality
cerebellar vermis	UBERON:0004720	94.09	gold quality
frontal cortex	UBERON:0001870	93.74	gold quality
adult organism	UBERON:0007023	93.71	gold quality
cerebellum	UBERON:0002037	93.42	gold quality
cerebellar cortex	UBERON:0002129	93.25	gold quality
cerebellar hemisphere	UBERON:0002245	93.23	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.14	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.92	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.79	gold quality
neocortex	UBERON:0001950	92.12	gold quality
nasal cavity mucosa	UBERON:0001826	92.06	gold quality
right frontal lobe	UBERON:0002810	91.92	gold quality
cerebral cortex	UBERON:0000956	91.76	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-11121	yes	269.25
E-GEOD-137537	yes	14.42
E-ANND-3	yes	8.69
E-ENAD-17	no	191.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

100 targeting SLC60A1, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
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-4775	99.98	75.00	6394
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-6809-3P	99.91	71.45	3814

Literature-anchored findings (GeneRIF, showing 2)

• Low MFSD4 expression is associated with hepatic metastasis in patients gastric cancer. (PMID:26872374)
• propose MFSD4A and MFSD9 to be novel transporters, belonging to disparate SLC families. Both proteins were located to neurons in mouse brain, and their mRNA expression levels were affected by the diet (PMID:29049335)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	mfsd4ab	ENSDARG00000008263
danio_rerio	mfsd4aa	ENSDARG00000023768
mus_musculus	Mfsd4a	ENSMUSG00000059149
rattus_norvegicus	Mfsd4a	ENSRNOG00000024657

Paralogs (1): MFSD4B (ENSG00000173214)

Protein

Protein identifiers

Solute carrier family 60 member 1 — Q8N468 (reviewed: Q8N468)

Alternative names: Major facilitator superfamily domain-containing protein 4, Major facilitator superfamily domain-containing protein 4A

All UniProt accessions (7): A0A087WUK7, A0A087WWW5, A0A087WYZ8, Q8N468, A0A087X0S2, B7Z8X0, F5H391

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SLC60A transporter family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N468-1	1	yes
Q8N468-2	2

RefSeq proteins (1): NP_857595* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011701	MFS	Family
IPR036259	MFS_trans_sf	Homologous_superfamily

Pfam: PF07690

UniProt features (18 total): transmembrane region 12, sequence variant 2, chain 1, glycosylation site 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N468-F1	77.09	0.53

Functional residue map

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

Glycosylation sites (1): 177

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): BENPORATH_ES_WITH_H3K27ME3, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, SABATES_COLORECTAL_ADENOMA_DN, VECCHI_GASTRIC_CANCER_EARLY_DN, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, GOBP_TRANSMEMBRANE_TRANSPORT, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOMF_TRANSPORTER_ACTIVITY, YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP, MEISSNER_NPC_HCP_WITH_H3K4ME2, RICKMAN_HEAD_AND_NECK_CANCER_E, MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, AKT_UP.V1_UP, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP, CRX_DN.V1_DN

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

GO Molecular Function (1): transmembrane transporter activity (GO:0022857)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
transporter activity	1
transmembrane transport	1
cellular anatomical structure	1

Protein interactions and networks

STRING

300 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC60A1	IQANK1	A8MXQ7	571
SLC60A1	ZNF284	Q2VY69	418
SLC60A1	KRABD2	Q6ZNG9	380
SLC60A1	GPR155	Q7Z3F1	377
SLC60A1	PCDHGB5	Q9Y5G0	371
SLC60A1	SLC67A2	Q8NBP5	370
SLC60A1	NXPE1	Q8N323	359
SLC60A1	NUDT13	Q86X67	348
SLC60A1	SCNN1A	P37088	339
SLC60A1	CBY1	Q9Y3M2	338
SLC60A1	LRRC37B	Q96QE4	326
SLC60A1	TMEM54	Q969K7	321
SLC60A1	CCDC28A	Q8IWP9	314
SLC60A1	VILL	O15195	311
SLC60A1	INHBA	P08476	306

IntAct

7 interactions, top by confidence:

A	B	Type	Score
MFSD4A	HIP1R	psi-mi:“MI:0914”(association)	0.530
MFSD4A	CHRM4	psi-mi:“MI:0915”(physical association)	0.370
MFSD4A	UBXN8	psi-mi:“MI:0914”(association)	0.350
MFSD4A	TIMM23	psi-mi:“MI:0914”(association)	0.350

BioGRID (280): SMAP2 (Affinity Capture-MS), CYSTM1 (Affinity Capture-MS), ATP5S (Affinity Capture-MS), GOLGA7 (Affinity Capture-MS), SLC25A24 (Affinity Capture-MS), ABHD17B (Affinity Capture-MS), GK (Affinity Capture-MS), HIP1R (Affinity Capture-MS), SLC7A2 (Affinity Capture-MS), APOB (Affinity Capture-MS), LGALS3 (Affinity Capture-MS), ATP11C (Affinity Capture-MS), MFSD4 (Affinity Capture-MS), MFSD4 (Two-hybrid), ATP5S (Affinity Capture-MS)

ESM2 similar proteins: A1DWM3, A4IF94, A4IHK6, A4QN56, A9JTG4, B0UYT5, B1AT66, B2RXV4, G8XYX6, O70324, O75387, P36021, P70187, Q0P5V9, Q0VCM6, Q1LUQ4, Q4LE88, Q569T7, Q5BIZ0, Q5BKX6, Q5J316, Q5RCN7, Q5RF58, Q5VW38, Q5XGZ9, Q68EU6, Q6DBX0, Q6P6V6, Q6PDC8, Q6ZSM3, Q6ZSS7, Q7SXB7, Q8BSM7, Q8CA03, Q8CBH5, Q8CGA3, Q8K1P8, Q8N370, Q8N468, Q8NBP5

Diamond homologs: A9JTG4, Q5BIZ0, Q5RCN7, Q6PDC8, Q7SXB7, Q80T22, Q8N468

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	3
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1850 predictions. Top by Δscore:

Variant	Effect	Δscore
1:205569295:AGGAC:A	donor_gain	1.0000
1:205569296:GGAC:G	donor_gain	1.0000
1:205569296:GGACG:G	donor_gain	1.0000
1:205569297:GAC:G	donor_gain	1.0000
1:205569297:GACG:G	donor_gain	1.0000
1:205569300:G:GG	donor_gain	1.0000
1:205579746:TGCA:T	acceptor_loss	1.0000
1:205579747:GCA:G	acceptor_loss	1.0000
1:205579748:CAGCC:C	acceptor_loss	1.0000
1:205579749:A:AG	acceptor_gain	1.0000
1:205579749:A:T	acceptor_loss	1.0000
1:205579749:AGCCT:A	acceptor_gain	1.0000
1:205579750:G:GA	acceptor_gain	1.0000
1:205579750:GC:G	acceptor_gain	1.0000
1:205579750:GCC:G	acceptor_gain	1.0000
1:205579750:GCCT:G	acceptor_gain	1.0000
1:205579750:GCCTG:G	acceptor_gain	1.0000
1:205579801:T:TA	acceptor_gain	1.0000
1:205579946:CCAG:C	donor_loss	1.0000
1:205579950:G:A	donor_loss	1.0000
1:205580922:G:GG	donor_gain	1.0000
1:205582232:G:GT	donor_gain	1.0000
1:205584081:G:GT	donor_gain	1.0000
1:205584082:A:T	donor_gain	1.0000
1:205586028:CCACA:C	acceptor_loss	1.0000
1:205586029:CACA:C	acceptor_loss	1.0000
1:205586031:CA:C	acceptor_loss	1.0000
1:205586032:A:AG	acceptor_gain	1.0000
1:205586032:AG:A	acceptor_gain	1.0000
1:205586033:G:C	acceptor_loss	1.0000

AlphaMissense

3319 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:205569148:A:C	S27R	0.999
1:205569150:C:A	S27R	0.999
1:205569150:C:G	S27R	0.999
1:205580697:A:C	S156R	0.999
1:205580699:C:A	S156R	0.999
1:205580699:C:G	S156R	0.999
1:205569154:G:C	G29R	0.998
1:205569155:G:A	G29D	0.998
1:205580686:G:A	G152D	0.998
1:205569136:A:C	S23R	0.997
1:205569138:C:A	S23R	0.997
1:205569138:C:G	S23R	0.997
1:205569194:T:C	L42P	0.997
1:205579878:G:C	G120R	0.997
1:205580685:G:C	G152R	0.997
1:205592233:A:C	S415R	0.997
1:205592235:C:A	S415R	0.997
1:205592235:C:G	S415R	0.997
1:205569133:T:A	W22R	0.996
1:205569133:T:C	W22R	0.996
1:205569155:G:T	G29V	0.996
1:205569158:T:C	L30P	0.996
1:205579866:G:C	G116R	0.996
1:205579901:C:A	N127K	0.996
1:205579901:C:G	N127K	0.996
1:205580898:T:C	F223L	0.996
1:205580900:C:A	F223L	0.996
1:205580900:C:G	F223L	0.996
1:205569151:T:C	F28L	0.995
1:205569153:C:A	F28L	0.995

dbSNP variants (sampled 300 via entrez): RS1000004555 (1:205582394 CAT>C), RS1000034645 (1:205572856 G>A), RS1000250374 (1:205591261 T>C), RS1000280364 (1:205603150 T>C), RS1000281579 (1:205590942 T>A,C), RS1000310749 (1:205580609 C>CG), RS1000424145 (1:205588045 G>C,T), RS1000482396 (1:205599393 C>T), RS1000544589 (1:205568036 G>A), RS1000588001 (1:205592718 G>A), RS1000619044 (1:205592524 C>G), RS1000808111 (1:205598358 A>C), RS1000870620 (1:205594430 T>G), RS1000906351 (1:205598628 C>G,T), RS1001272197 (1:205588333 G>T)

Disease associations

OMIM: gene MIM:620299 | 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
GCST008058_236	Estimated glomerular filtration rate	1.000000e-08
GCST008059_222	Estimated glomerular filtration rate	3.000000e-07

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

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	3
Formaldehyde	decreases expression, increases expression	2
Nickel	decreases expression	2
uranyl acetate	affects expression	1
propionaldehyde	increases expression	1
N-acetyl-4-benzoquinoneimine	affects response to substance	1
aflatoxin B2	affects methylation	1
CGP 52608	increases reaction, affects binding	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Zoledronic Acid	decreases expression	1
Cisplatin	increases expression, affects cotreatment	1
Ethyl Methanesulfonate	increases expression	1
Folic Acid	decreases expression	1
Lipopolysaccharides	increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Triclosan	increases expression	1
Uranium	affects expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	affects methylation	1
Asbestos, Serpentine	decreases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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