MFSD12

gene
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Also known as MGC20700PP3501SLC59B1

Summary

MFSD12 (major facilitator superfamily domain containing 12, HGNC:28299) is a protein-coding gene on chromosome 19p13.3, encoding Major facilitator superfamily domain-containing protein 12 (Q6NUT3). Transporter that mediates the import of cysteine into melanosomes, thereby regulating skin pigmentation.

Enables cysteine transmembrane transporter activity. Involved in cysteine transmembrane transport; pigment metabolic process involved in pigmentation; and regulation of melanin biosynthetic process. Located in lysosome and melanosome. Part of late endosome.

Source: NCBI Gene 126321 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 44 total
  • MANE Select transcript: NM_174983

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28299
Approved symbolMFSD12
Namemajor facilitator superfamily domain containing 12
Location19p13.3
Locus typegene with protein product
StatusApproved
AliasesMGC20700, PP3501, SLC59B1
Ensembl geneENSG00000161091
Ensembl biotypeprotein_coding
OMIM617745
Entrez126321

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 8 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000355415, ENST00000398558, ENST00000585788, ENST00000585814, ENST00000586402, ENST00000588626, ENST00000588918, ENST00000589063, ENST00000589157, ENST00000589995, ENST00000591878, ENST00000592652, ENST00000615073, ENST00000913269, ENST00000951867

RefSeq mRNA: 2 — MANE Select: NM_174983 NM_001287529, NM_174983

CCDS: CCDS42465, CCDS74256

Canonical transcript exons

ENST00000355415 — 10 exons

ExonStartEnd
ENSE0000111526835462553546425
ENSE0000111527135472723547364
ENSE0000114843735460743546168
ENSE0000140244635571063557586
ENSE0000140770735441993544732
ENSE0000224776035448093544939
ENSE0000345911535481233548267
ENSE0000351569535509843551194
ENSE0000361911235474553547547
ENSE0000362010435478483548030

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 96.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 67.3401 / max 2705.6961, expressed in 1817 samples.

FANTOM5 promoters (22 alternative TSS)

Promoter IDTPM avgSamples expressed
17830356.97381813
1783023.7720178
1783042.90521259
1783171.0760482
1782980.6511255
1782990.4423156
1783150.411858
1783070.260864
1782940.142155
1783140.125643

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225596.92gold quality
metanephros cortexUBERON:001053396.63gold quality
right uterine tubeUBERON:000130296.42gold quality
right hemisphere of cerebellumUBERON:001489096.14gold quality
cerebellar hemisphereUBERON:000224595.41gold quality
granulocyteCL:000009495.37gold quality
C1 segment of cervical spinal cordUBERON:000646995.27gold quality
cerebellar cortexUBERON:000212995.17gold quality
adenohypophysisUBERON:000219694.67gold quality
body of pancreasUBERON:000115094.65gold quality
right lobe of thyroid glandUBERON:000111994.37gold quality
right frontal lobeUBERON:000281094.28gold quality
left lobe of thyroid glandUBERON:000112093.94gold quality
monocyteCL:000057693.87gold quality
mononuclear cellCL:000084293.69gold quality
leukocyteCL:000073893.56gold quality
small intestine Peyer’s patchUBERON:000345493.56gold quality
tibial nerveUBERON:000132393.30gold quality
lower esophagus mucosaUBERON:003583493.20gold quality
skin of legUBERON:000151193.06gold quality
minor salivary glandUBERON:000183092.94gold quality
pituitary glandUBERON:000000792.82gold quality
left adrenal gland cortexUBERON:003582592.75gold quality
spinal cordUBERON:000224092.64gold quality
thyroid glandUBERON:000204692.56gold quality
spleenUBERON:000210692.46gold quality
right coronary arteryUBERON:000162592.37gold quality
skin of abdomenUBERON:000141692.35gold quality
body of stomachUBERON:000116192.32gold quality
lower esophagus muscularis layerUBERON:003583392.32gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-8142yes18.25
E-ANND-3yes7.50
E-CURD-112yes3.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting MFSD12, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-6752-3P99.7266.711587
HSA-MIR-520A-5P99.3566.721632
HSA-MIR-525-5P99.3566.851615
HSA-MIR-450599.2767.812678
HSA-MIR-578799.2267.862628
HSA-MIR-6846-5P98.8165.861121
HSA-MIR-6848-5P98.8165.491126
HSA-MIR-423-5P98.6967.481522
HSA-MIR-3184-5P98.5667.131491
HSA-MIR-615-5P98.1063.76591
HSA-MIR-519496.7763.911021
HSA-MIR-6738-5P96.3363.61815
HSA-MIR-1266-3P96.2366.36778
HSA-MIR-6734-5P95.7065.56950
HSA-MIR-1914-3P95.0763.37762

Literature-anchored findings (GeneRIF, showing 4)

  • pp3501 inhibited the proliferation of SH-SY5Y cells, arrested the cell cycle at G1 phase, and sensitized the SH-SY5Y cells to sodium butyrate treatment. (PMID:22441875)
  • Elevated MFSD12 expression promotes melanoma cell proliferation, and MFSD12 is a valuable prognostic biomarker and promising therapeutic target in melanoma. (PMID:30385854)
  • MFSD12 mediates the import of cysteine into melanosomes and lysosomes. (PMID:33208952)
  • Major Facilitator Superfamily Domain Containing 12 Is Overexpressed in Lung Cancer and Exhibits an Oncogenic Role in Lung Adenocarcinoma Cells. (PMID:38687351)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriomfsd12aENSDARG00000061908
mus_musculusMfsd12ENSMUSG00000034854
rattus_norvegicusMfsd12ENSRNOG00000039858
caenorhabditis_elegansWBGENE00017530

Paralogs (2): MFSD2A (ENSG00000168389), MFSD2B (ENSG00000205639)

Protein

Protein identifiers

Major facilitator superfamily domain-containing protein 12Q6NUT3 (reviewed: Q6NUT3)

All UniProt accessions (8): Q6NUT3, A0A087WU85, A0A0A0MS91, K7EJS5, K7EKU1, K7ENE1, K7EQ22, K7ERJ8

UniProt curated annotations — full annotation on UniProt →

Function. Transporter that mediates the import of cysteine into melanosomes, thereby regulating skin pigmentation. In melanosomes, cysteine import is required both for normal levels of cystine, the oxidized dimer of cysteine, and provide cysteine for the production of the cysteinyldopas used in pheomelanin synthesis, thereby regulating skin pigmentation. Also catalyzes import of cysteine into lysosomes in non-pigmented cells, regulating lysosomal cystine and cysteine storage, which is essnetial for redox homeostasis.

Subcellular location. Melanosome membrane. Lysosome membrane.

Tissue specificity. Widely expressed, with high expression in primary melanocytes.

Post-translational modifications. Phosphorylation at Thr-254 by MTOR via mTORC1 pathway promotes cysteine transport in lysosomes, thereby regulating lysosomal cysteine and cystine storage and redox homeostasis.

Polymorphism. Genetic variants in MFSD12 cause skin pigmentation variation. Skin pigmentation is among the most visible examples of human phenotypic variation, with a broad normal range that is subject to substantial geographic stratification. In the case of skin, individuals tend to have lighter pigmentation with increasing distance from the equator. His-192 is commonly found in East Asians and Native Americans only, and significantly correlates with lower solar radiation intensity in East Asia.

Similarity. Belongs to the major facilitator superfamily.

Isoforms (4)

UniProt IDNamesCanonical?
Q6NUT3-11yes
Q6NUT3-22
Q6NUT3-33
Q6NUT3-44

RefSeq proteins (2): NP_001274458, NP_778148* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR036259MFS_trans_sfHomologous_superfamily
IPR039672MFS_2Family

Pfam: PF13347

Catalyzed reactions (Rhea), 1 shown:

  • L-cysteine(in) = L-cysteine(out) (RHEA:29655)

UniProt features (43 total): topological domain 12, transmembrane region 12, mutagenesis site 7, sequence variant 5, splice variant 3, modified residue 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6NUT3-F184.770.57

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 (2): 1, 254

Mutagenesis-validated functional residues (7):

PositionPhenotype
13does not affect phosphorylation by mtor.
73does not affect phosphorylation by mtor.
113does not affect phosphorylation by mtor.
122does not affect phosphorylation by mtor.
254abolished phosphorylation by mtor; dominant-negative inhibitor of cysteine transporter activity.
254mimics phosphorylation; enhanced cysteine and cystine storage in lysosomes.
256–257reduced localization to lysosomes and redirection to the cell membrane.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 172 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_PHENOL_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_TRANSPORT, GOBP_PHENOL_CONTAINING_COMPOUND_BIOSYNTHETIC_PROCESS, GOCC_VACUOLAR_MEMBRANE, GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, GOBP_ORGANIC_ACID_TRANSPORT, GOBP_PIGMENTATION, GOBP_AMINO_ACID_TRANSPORT, GOBP_ORGANIC_ANION_TRANSPORT, GOBP_SULFUR_COMPOUND_TRANSPORT, GOBP_PIGMENT_METABOLIC_PROCESS, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, GOBP_ORGANIC_CATION_TRANSPORT, GOBP_PIGMENT_BIOSYNTHETIC_PROCESS

GO Biological Process (8): carbohydrate transport (GO:0008643), melanin biosynthetic process (GO:0042438), pigment metabolic process involved in pigmentation (GO:0043474), regulation of melanin biosynthetic process (GO:0048021), negative regulation of melanin biosynthetic process (GO:0048022), L-cysteine transmembrane transport (GO:1903712), amino acid transport (GO:0006865), transmembrane transport (GO:0055085)

GO Molecular Function (3): symporter activity (GO:0015293), L-cysteine transmembrane transporter activity (GO:0033229), protein binding (GO:0005515)

GO Cellular Component (7): lysosome (GO:0005764), lysosomal membrane (GO:0005765), late endosome (GO:0005770), plasma membrane (GO:0005886), melanosome membrane (GO:0033162), melanosome (GO:0042470), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport3
melanin biosynthetic process2
melanin metabolic process1
secondary metabolite biosynthetic process1
pigment biosynthetic process1
phenol-containing compound biosynthetic process1
pigment metabolic process1
pigmentation1
regulation of secondary metabolite biosynthetic process1
regulation of melanin biosynthetic process1
negative regulation of secondary metabolite biosynthetic process1
L-cysteine transport1
L-alpha-amino acid transmembrane transport1
cellular process1
secondary active transmembrane transporter activity1
sulfur amino acid transmembrane transporter activity1
neutral L-amino acid transmembrane transporter activity1
L-amino acid transmembrane transporter activity1
L-cysteine transmembrane transport1
binding1
lytic vacuole1
lysosome1
lytic vacuole membrane1
endosome1
membrane1
cell periphery1
melanosome1
chitosome1
pigment granule membrane1
pigment granule1
cellular anatomical structure1

Protein interactions and networks

STRING

764 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MFSD12SLC45A2Q9UMX9689
MFSD12SLC67A2Q8NBP5639
MFSD12MFSD6LQ8IWD5625
MFSD12MFSD11O43934624
MFSD12SLC24A5Q71RS6609
MFSD12SLC68A1Q14CX5606
MFSD12MFSD6Q6ZSS7578
MFSD12SLC75A1Q14728537
MFSD12UNC93AQ86WB7530
MFSD12OCA2Q04671527
MFSD12MFSD8Q8NHS3515
MFSD12SLC61A1Q6N075511
MFSD12TMEM132EQ6IEE7498
MFSD12TLCD3AQ8TBR7493
MFSD12TPCN2Q8NHX9492

IntAct

26 interactions, top by confidence:

ABTypeScore
NIPAL1ESYT2psi-mi:“MI:0914”(association)0.640
SLC39A4TMEM120Bpsi-mi:“MI:0914”(association)0.530
SLC22A9GPR89Apsi-mi:“MI:0914”(association)0.530
MFSD12ADRB2psi-mi:“MI:0915”(physical association)0.370
Nrip3ILVBLpsi-mi:“MI:0914”(association)0.350
Npc1ESYT2psi-mi:“MI:0914”(association)0.350
TTYH1TMEM223psi-mi:“MI:0914”(association)0.350
TSPAN15TMEM223psi-mi:“MI:0914”(association)0.350
BSCL2TMEM223psi-mi:“MI:0914”(association)0.350
CRELD1TMEM223psi-mi:“MI:0914”(association)0.350
GPR17TMEM120Bpsi-mi:“MI:0914”(association)0.350
TSPAN31TMEM120Bpsi-mi:“MI:0914”(association)0.350
OPRL1METTL15psi-mi:“MI:0914”(association)0.350
SCN4AC2CD4Bpsi-mi:“MI:0914”(association)0.350
SLC22A4RTL8Cpsi-mi:“MI:0914”(association)0.350
TMEM169GPR89Apsi-mi:“MI:0914”(association)0.350
SLC5A6SLC31A1psi-mi:“MI:0914”(association)0.350
SLC26A6SLC25A17psi-mi:“MI:0914”(association)0.350
PMELMAN1A2psi-mi:“MI:0914”(association)0.350
SYPL2TSPAN15psi-mi:“MI:0914”(association)0.350
UPK1AMFSD12psi-mi:“MI:0914”(association)0.350
SLCO4C1SLC9A1psi-mi:“MI:0914”(association)0.350
LDLRAD1ZNF316psi-mi:“MI:0914”(association)0.350
MFSD12SNAP23psi-mi:“MI:0914”(association)0.350

BioGRID (92): MFSD12 (Affinity Capture-MS), MFSD12 (Synthetic Growth Defect), MFSD12 (Affinity Capture-MS), MFSD12 (Affinity Capture-MS), MFSD12 (Affinity Capture-MS), MFSD12 (Affinity Capture-MS), MFSD12 (Affinity Capture-MS), MFSD12 (Affinity Capture-MS), MFSD12 (Two-hybrid), MFSD12 (Two-hybrid), SSMEM1 (Two-hybrid), MFSD12 (Two-hybrid), MFSD12 (Affinity Capture-MS), MFSD12 (Affinity Capture-RNA), MFSD12 (Affinity Capture-MS)

ESM2 similar proteins: A0A3Q2HW92, A6NDV4, A6NFX1, A6QLK4, B1AWJ5, F1NCD6, F1NJ67, F1PZV2, O35308, O35595, O70461, O95907, Q08DX7, Q0IHM1, Q0P5C0, Q0P5M9, Q13286, Q14728, Q29611, Q2YDU8, Q3T9M1, Q3U481, Q501I9, Q5R8G5, Q5R9A1, Q5U419, Q60HH0, Q61124, Q66H95, Q6NUT3, Q6UXD7, Q6ZMD2, Q7RTT9, Q8BFQ6, Q8CE47, Q8NA29, Q8R0G7, Q8R139, Q8TB61, Q8VCW4

Diamond homologs: A0A3Q2HW92, F1PZV2, Q3U481, Q6NUT3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
SLC-mediated transmembrane transport616.9×9e-05
Transport of small molecules67.2×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance10
Likely benign5
Benign5

Top pathogenic / likely-pathogenic (0)

SpliceAI

2316 predictions. Top by Δscore:

VariantEffectΔscore
19:3543233:A:AGacceptor_gain1.0000
19:3543233:AGC:Aacceptor_gain1.0000
19:3543234:G:GGacceptor_gain1.0000
19:3543234:GC:Gacceptor_gain1.0000
19:3543234:GCG:Gacceptor_gain1.0000
19:3543234:GCGAT:Gacceptor_gain1.0000
19:3543252:T:TAacceptor_gain1.0000
19:3543453:G:GGdonor_gain1.0000
19:3546068:ACTC:Adonor_loss1.0000
19:3546069:CTCA:Cdonor_loss1.0000
19:3546070:TCA:Tdonor_loss1.0000
19:3546072:A:ACdonor_gain1.0000
19:3546072:ACG:Adonor_loss1.0000
19:3546072:ACGGG:Adonor_gain1.0000
19:3546073:C:CTdonor_gain1.0000
19:3546073:CG:Cdonor_gain1.0000
19:3546073:CGG:Cdonor_gain1.0000
19:3546073:CGGG:Cdonor_gain1.0000
19:3546073:CGGGC:Cdonor_gain1.0000
19:3546164:CTGTT:Cacceptor_gain1.0000
19:3546165:TGTT:Tacceptor_gain1.0000
19:3546166:GTT:Gacceptor_gain1.0000
19:3546167:TT:Tacceptor_gain1.0000
19:3546169:C:CCacceptor_gain1.0000
19:3546170:T:Gacceptor_loss1.0000
19:3546171:G:Cacceptor_gain1.0000
19:3546249:CCCTA:Cdonor_loss1.0000
19:3546250:CCTAC:Cdonor_loss1.0000
19:3546252:TAC:Tdonor_loss1.0000
19:3546253:A:ACdonor_gain1.0000

AlphaMissense

3052 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:3550984:C:AR170M0.998
19:3551069:A:GW142R0.998
19:3551069:A:TW142R0.998
19:3546136:G:CS409R0.997
19:3546136:G:TS409R0.997
19:3546138:T:GS409R0.997
19:3557284:G:CF40L0.997
19:3557284:G:TF40L0.997
19:3557286:A:GF40L0.997
19:3557308:G:CN32K0.997
19:3557308:G:TN32K0.997
19:3547509:G:CN292K0.996
19:3547509:G:TN292K0.996
19:3547522:C:AR288M0.996
19:3548247:G:TA177D0.996
19:3550996:A:GL166P0.996
19:3551044:A:GL150P0.996
19:3551194:C:TG100D0.996
19:3557106:C:GG100R0.996
19:3557211:C:GG65R0.996
19:3557289:A:GW39R0.996
19:3557289:A:TW39R0.996
19:3557306:T:AD33V0.996
19:3557307:C:GD33H0.996
19:3557322:C:GG28R0.996
19:3546124:C:AK413N0.995
19:3546124:C:GK413N0.995
19:3546271:A:GL393P0.995
19:3547326:G:CS323R0.995
19:3547326:G:TS323R0.995

dbSNP variants (sampled 300 via entrez): RS1000194338 (19:3555253 C>T), RS1000536816 (19:3546863 T>C), RS1000618834 (19:3553326 G>A), RS1000803191 (19:3554195 G>A,T), RS1000861814 (19:3539048 C>A,G,T), RS1000865743 (19:3552763 A>G), RS1000999840 (19:3544553 TGCCCTCACCC>T), RS1001138191 (19:3544429 A>G), RS1001146108 (19:3557417 C>T), RS1001295935 (19:3541534 G>A), RS1001367325 (19:3542627 C>T), RS1001473630 (19:3551639 C>T), RS1001481416 (19:3542496 C>CA), RS1001506248 (19:3554462 A>G), RS1001572870 (19:3545885 T>G)

Disease associations

OMIM: gene MIM:617745 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST007452_13Skin pigmentation2.000000e-10
GCST008516_10Skin pigmentation (conditioned on rs1426654 and rs35397)6.000000e-09
GCST008516_3Skin pigmentation (conditioned on rs1426654 and rs35397)2.000000e-08
GCST010303_58Nevus count or cutaneous melanoma2.000000e-09
GCST010304_9Cutaneous malignant melanoma4.000000e-10
GCST90002283_7Facial pigmentation measurement (UV light)1.000000e-08
GCST90002284_7Facial pigmentation measurement (polar light)2.000000e-14

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004632nevus count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression, increases methylation4
Acetaminophenincreases expression2
Estradiolaffects cotreatment, increases expression2
Cadmium Chlorideincreases abundance, increases expression2
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
sodium arsenitedecreases expression1
butyraldehydeincreases expression1
K 7174increases expression1
abrineincreases expression1
MT19c compounddecreases expression1
Sunitinibdecreases expression1
Cadmiumincreases abundance, increases expression1
Cisplatindecreases expression1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Phthalic Acidsincreases methylation1
Smokedecreases expression1
Thiramincreases expression1
Tretinoinincreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Antirheumatic Agentsdecreases expression1
Okadaic Acidincreases expression1
Copper Sulfateincreases expression1
Lactic Acidincreases expression1
Acrylamidedecreases expression1
Volatile Organic Compoundsaffects expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D4GBHCT116-MFSD12-KO-c10Cancer cell lineMale
CVCL_D4GCHCT116-MFSD12-KO-c9Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.