LYSET

gene
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Also known as DKFZP564F1123GCAF

Summary

LYSET (lysosomal enzyme trafficking factor, HGNC:20218) is a protein-coding gene on chromosome 14q32.12, encoding Lysosomal enzyme trafficking factor (Q8N6I4). Required for mannose-6-phosphate-dependent trafficking of lysosomal enzymes.

Involved in lysosomal transport; lysosome organization; and regulation of vesicle-mediated transport. Located in Golgi cisterna.

Source: NCBI Gene 26175 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): dysostosis multiplex, Ain-Naz type (Strong, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 30 total — 1 pathogenic, 2 likely-pathogenic
  • MANE Select transcript: NM_001098621

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20218
Approved symbolLYSET
Namelysosomal enzyme trafficking factor
Location14q32.12
Locus typegene with protein product
StatusApproved
AliasesDKFZP564F1123, GCAF
Ensembl geneENSG00000153485
Ensembl biotypeprotein_coding
OMIM619332
Entrez26175

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000283534, ENST00000415050, ENST00000857222, ENST00000928792, ENST00000928793, ENST00000928794

RefSeq mRNA: 2 — MANE Select: NM_001098621 NM_001098621, NM_015676

CCDS: CCDS41980, CCDS45158

Canonical transcript exons

ENST00000415050 — 2 exons

ExonStartEnd
ENSE000016873529318626093188463
ENSE000017453979318531793185485

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 93.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.4689 / max 482.8426, expressed in 1777 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1411639.19721770
1411674.3490520
1411650.3243137
1411660.3104137
1411680.288197

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
islet of LangerhansUBERON:000000693.31gold quality
mucosa of transverse colonUBERON:000499192.19gold quality
rectumUBERON:000105290.57gold quality
endometriumUBERON:000129590.14gold quality
monocyteCL:000057689.99gold quality
adult mammalian kidneyUBERON:000008289.93gold quality
ventricular zoneUBERON:000305389.93gold quality
leukocyteCL:000073889.90gold quality
apex of heartUBERON:000209889.65gold quality
gastrocnemiusUBERON:000138889.52gold quality
right adrenal gland cortexUBERON:003582789.52gold quality
pancreasUBERON:000126489.27gold quality
right adrenal glandUBERON:000123389.26gold quality
muscle of legUBERON:000138389.15gold quality
heart left ventricleUBERON:000208489.13gold quality
transverse colonUBERON:000115788.96gold quality
left adrenal glandUBERON:000123488.95gold quality
prostate glandUBERON:000236788.92gold quality
left adrenal gland cortexUBERON:003582588.84gold quality
cortex of kidneyUBERON:000122588.80gold quality
body of pancreasUBERON:000115088.78gold quality
metanephros cortexUBERON:001053388.77gold quality
embryoUBERON:000092288.55gold quality
ganglionic eminenceUBERON:000402388.55gold quality
cortical plateUBERON:000534388.34gold quality
duodenumUBERON:000211488.22gold quality
fundus of stomachUBERON:000116088.09gold quality
kidneyUBERON:000211387.87gold quality
adrenal glandUBERON:000236987.65gold quality
hindlimb stylopod muscleUBERON:000425287.63gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.85
E-MTAB-7303no155.77
E-MTAB-6379no141.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting LYSET, 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-126-5P100.0072.713180
HSA-MIR-186-5P99.9970.833707
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-314899.9775.066478
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-590-3P99.9674.346478
HSA-MIR-576-5P99.8470.462582
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-2681-5P99.7567.641655
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-120099.7170.421838
HSA-MIR-548AU-3P99.7068.221373
HSA-MIR-509399.6769.262291
HSA-MIR-378A-5P99.6566.331311
HSA-MIR-3679-3P99.6469.881599
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-432899.5771.064094
HSA-MIR-17-3P99.5566.771311
HSA-MIR-1212399.5271.792990
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-548AV-3P99.4368.501721
HSA-MIR-513A-3P99.3970.633620
HSA-MIR-513C-3P99.3970.633620
HSA-MIR-6853-3P99.3670.791558
HSA-MIR-442799.3470.331854
HSA-MIR-120699.3069.321016

Literature-anchored findings (GeneRIF, showing 4)

  • Biallelic TMEM251 variants in patients with severe skeletal dysplasia and extreme short stature. (PMID:33252156)
  • The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. (PMID:36074821)
  • Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins. (PMID:36074822)
  • LYSET/TMEM251- a novel key component of the mannose 6-phosphate pathway. (PMID:36633450)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotmem251ENSDARG00000042341
mus_musculusLysetENSMUSG00000046675
rattus_norvegicusLysetENSRNOG00000008101

Protein

Protein identifiers

Lysosomal enzyme trafficking factorQ8N6I4 (reviewed: Q8N6I4)

Alternative names: GNPTAB cleavage and activity factor, Transmembrane protein 251

All UniProt accessions (1): Q8N6I4

UniProt curated annotations — full annotation on UniProt →

Function. Required for mannose-6-phosphate-dependent trafficking of lysosomal enzymes. LYSET bridges GlcNAc-1-phosphate transferase (GNPTAB), to the membrane-bound transcription factor site-1 protease (MBTPS1), thus allowing proteolytic activation of the GNPTAB. GNPTAB is involved in the regulation of M6P-dependent Golgi-to-lysosome trafficking of lysosomal enzymes. LYSET is thus an essential factor for maturation and delivery of lysosomal hydrolases. (Microbial infection) Essential for infection by muliple viruses, including SARS-CoV-2, that utilize activated cathepsins for entry after M6P-dependent lysosomal transport.

Subunit / interactions. Interacts with GNPTAB; this interaction is important for proper localization of GNPTAB in Golgi stacks. Interacts with MBTPS1.

Subcellular location. Golgi apparatus membrane.

Disease relevance. Dysostosis multiplex, Ain-Naz type (DMAN) [MIM:619345] An autosomal recessive, severe skeletal disease characterized by features of dysostosis multiplex, severe short stature, coarse facies with broad nose and prominent lips, protruding abdomens, and progressive skeletal changes causing gradual mobility loss. Death in childhood or early adulthood may occur. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the LYSET family.

Isoforms (3)

UniProt IDNamesCanonical?
Q8N6I4-11yes
Q8N6I4-22
Q8N6I4-33

RefSeq proteins (2): NP_001092091, NP_056491 (=MANE)

Domains & families (InterPro)

IDNameType
IPR028024LYSETFamily

Pfam: PF15190

UniProt features (11 total): mutagenesis site 3, transmembrane region 2, splice variant 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N6I4-F163.230.00

Functional residue map

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

Mutagenesis-validated functional residues (3):

PositionPhenotype
86rescues the lysosomal trafficking defect in lyset-deficient cells.
136rescues the lysosomal trafficking defect in lyset-deficient cells.
150rescues the lysosomal trafficking defect in lyset-deficient cells.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 179 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_LYSOSOMAL_TRANSPORT, GOBP_VACUOLE_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GOBP_PROTEIN_TARGETING, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_VACUOLAR_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_PROTEIN_LOCALIZATION_TO_LYSOSOME, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_VACUOLE, GOBP_REGULATION_OF_PROTEIN_STABILITY, SCHLOSSER_SERUM_RESPONSE_DN

GO Biological Process (7): protein targeting to lysosome (GO:0006622), lysosome organization (GO:0007040), lysosomal transport (GO:0007041), response to virus (GO:0009615), protein catabolic process (GO:0030163), regulation of protein stability (GO:0031647), regulation of vesicle-mediated transport (GO:0060627)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), Golgi cisterna (GO:0031985), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein targeting to vacuole1
lysosomal transport1
protein localization to lysosome1
lytic vacuole organization1
vacuolar transport1
response to other organism1
macromolecule catabolic process1
protein metabolic process1
regulation of biological quality1
vesicle-mediated transport1
regulation of cellular process1
regulation of transport1
binding1
Golgi apparatus1
bounding membrane of organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
Golgi stack1
Golgi apparatus subcompartment1
cellular anatomical structure1

Protein interactions and networks

STRING

266 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LYSETPWWP2BQ6NUJ5607
LYSETTAF5LO75529521
LYSETKRTAP4-8Q9BYQ9492
LYSETTMEM41BQ5BJD5474
LYSETACP1P24666473
LYSETZMYM2Q9UBW7471
LYSETKLHL42Q9P2K6394
LYSETDALRD3Q5D0E6380
LYSETWDR81Q562E7376
LYSETNAGPAQ9UK23375
LYSETWDR91A4D1P6375
LYSETYPEL1O60688368
LYSETVPS37AQ8NEZ2365
LYSETBORCS8Q96FH0365
LYSETSCAF4O95104359

IntAct

2 interactions, top by confidence:

ABTypeScore
TMED10PGRMC1psi-mi:“MI:0914”(association)0.350

BioGRID (7): TMEM251 (Negative Genetic), TMEM251 (Phenotypic Enhancement), TMEM251 (Affinity Capture-MS), TMEM251 (Affinity Capture-Western), GNPTAB (Affinity Capture-Western), GNPTG (Co-localization), GNPTAB (Co-localization)

ESM2 similar proteins: A0A7H0DNA7, A0A8I3NQW8, B2RWJ3, C4QVD6, C5DQY5, C7Z504, D1ZRK4, E9EM69, F1LXS7, F5HDD0, F8RT80, O36388, O48670, O94592, P0C655, P20987, P33835, P36707, Q04684, Q09366, Q09714, Q09952, Q09993, Q197D8, Q1KZ54, Q1L864, Q21642, Q28IL7, Q2H3I7, Q2M2T6, Q54U35, Q5M7C7, Q5M9B7, Q5XJX0, Q64919, Q6GNY6, Q6NVQ1, Q6Q7K0, Q6QA74, Q6ZWX0

Diamond homologs: F1LXS7, Q2HJ69, Q5HZT8, Q5TZA3, Q5ZLR7, Q66J17, Q6GLZ9, Q6QA74, Q8BH26, Q8N6I4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic2
Uncertain significance24
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
1120020NM_001098621.4(LYSET):c.115C>T (p.Arg39Trp)Pathogenic
1120021NM_001098621.4(LYSET):c.197dup (p.Tyr66Ter)Likely pathogenic
807354NM_001098621.4(LYSET):c.216dup (p.His73fs)Likely pathogenic

SpliceAI

384 predictions. Top by Δscore:

VariantEffectΔscore
14:93185029:G:GTdonor_gain0.9900
14:93185030:A:Tdonor_gain0.9900
14:93186251:A:AGacceptor_gain0.9900
14:93186255:TGAA:Tacceptor_loss0.9900
14:93186256:GAAG:Gacceptor_loss0.9900
14:93186258:A:ACacceptor_loss0.9900
14:93186430:G:GTdonor_gain0.9900
14:93186453:A:Tdonor_gain0.9900
14:93186457:C:Gdonor_gain0.9900
14:93186762:G:GTdonor_gain0.9900
14:93185028:GGAAG:Gdonor_gain0.9800
14:93185030:AAGGT:Adonor_loss0.9800
14:93185031:AGG:Adonor_loss0.9800
14:93185032:GGTGA:Gdonor_loss0.9800
14:93185033:GT:Gdonor_loss0.9800
14:93185034:T:Adonor_loss0.9800
14:93185467:G:GTdonor_gain0.9800
14:93185486:G:GGdonor_gain0.9800
14:93186255:T:TAacceptor_gain0.9800
14:93186258:A:AGacceptor_gain0.9800
14:93186259:G:GGacceptor_gain0.9800
14:93186431:A:Tdonor_gain0.9800
14:93186252:A:Gacceptor_gain0.9700
14:93186258:AG:Aacceptor_gain0.9700
14:93186259:GG:Gacceptor_gain0.9700
14:93185033:GTGAG:Gdonor_loss0.9600
14:93185482:CATT:Cdonor_gain0.9600
14:93186251:AATTT:Aacceptor_gain0.9600
14:93185433:C:Gdonor_gain0.9500
14:93185484:TT:Tdonor_gain0.9500

AlphaMissense

1095 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000116037 (14:93185023 G>C), RS1001228668 (14:93187353 G>A), RS1001434329 (14:93183483 A>G), RS1001484907 (14:93183908 C>T), RS1003021095 (14:93187667 T>A), RS1004292159 (14:93187544 A>G), RS1004788104 (14:93184405 C>T), RS1005153871 (14:93187741 C>T), RS1005566874 (14:93186082 G>C), RS1006076180 (14:93185743 T>G), RS1007087425 (14:93185077 C>T), RS1007491973 (14:93186304 G>A), RS1008486268 (14:93184468 C>G), RS1008582673 (14:93184721 G>A), RS1009207508 (14:93185342 C>T)

Disease associations

OMIM: gene MIM:619332 | disease phenotypes: MIM:619345

GenCC curated gene-disease

DiseaseClassificationInheritance
dysostosis multiplex, Ain-Naz typeStrongAutosomal recessive

Mondo (2): dysostosis multiplex, Ain-Naz type (MONDO:0859156), intellectual disability (MONDO:0001071)

Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST004823_4Cognitive function3.000000e-06
GCST005951_7Body mass index4.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0008354cognitive function measurement
EFO:0004340body mass index

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
dicrotophosdecreases expression1
bisphenol Aaffects cotreatment, increases methylation1
trichostatin Aaffects expression1
arseniteaffects binding, increases reaction1
abrineincreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophenincreases expression1
Doxorubicinincreases expression1
Progesteroneincreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoindecreases expression1
Urethanedecreases expression1
Valproic Acidincreases expression, decreases methylation1
Cyclosporineincreases expression1
Copper Sulfatedecreases expression1
Lactic Acidaffects expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E2M4HAP1 TMEM251 (-)Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394Not specifiedUNKNOWNFCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614Not specifiedCOMPLETEDPsychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405Not specifiedCOMPLETEDTMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders