GANAB

gene
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Also known as GluIIG2ANKIAA0088GIIAGIIalpha

Summary

GANAB (glucosidase II alpha subunit, HGNC:4138) is a protein-coding gene on chromosome 11q12.3, encoding Neutral alpha-glucosidase AB (Q14697). Catalytic subunit of glucosidase II that cleaves sequentially the 2 innermost alpha-1,3-linked glucose residues from the Glc(2)Man(9)GlcNAc(2) oligosaccharide precursor of immature glycoproteins. It is a selective cancer dependency (DepMap: 10.7% of cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This gene encodes the alpha subunit of glucosidase II and a member of the glycosyl hydrolase 31 family of proteins. The heterodimeric enzyme glucosidase II plays a role in protein folding and quality control by cleaving glucose residues from immature glycoproteins in the endoplasmic reticulum. Expression of the encoded protein is elevated in lung tumor tissue and in response to UV irradiation. Mutations in this gene cause autosomal-dominant polycystic kidney and liver disease.

Source: NCBI Gene 23193 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): polycystic kidney disease 3 with or without polycystic liver disease (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 9
  • Clinical variants (ClinVar): 631 total — 18 pathogenic, 33 likely-pathogenic
  • Phenotypes (HPO): 33
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 10.7% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_198334

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4138
Approved symbolGANAB
Nameglucosidase II alpha subunit
Location11q12.3
Locus typegene with protein product
StatusApproved
AliasesGluII, G2AN, KIAA0088, GIIA, GIIalpha
Ensembl geneENSG00000089597
Ensembl biotypeprotein_coding
OMIM104160
Entrez23193

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 15 protein_coding, 5 retained_intron, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000346178, ENST00000356638, ENST00000524437, ENST00000525994, ENST00000526210, ENST00000526392, ENST00000526732, ENST00000528503, ENST00000529737, ENST00000531563, ENST00000532402, ENST00000534419, ENST00000534422, ENST00000534613, ENST00000534779, ENST00000540933, ENST00000648273, ENST00000881668, ENST00000881669, ENST00000881670, ENST00000933198, ENST00000933199, ENST00000933200, ENST00000933201, ENST00000933202, ENST00000933203

RefSeq mRNA: 9 — MANE Select: NM_198334 NM_001278192, NM_001278193, NM_001278194, NM_001329222, NM_001329223, NM_001329224, NM_001329225, NM_198334, NM_198335

CCDS: CCDS41656, CCDS60817, CCDS60818, CCDS8026

Canonical transcript exons

ENST00000356638 — 24 exons

ExonStartEnd
ENSE000021446696262482962625924
ENSE000021966756264656262646613
ENSE000034651536263962762639731
ENSE000034663876263103062631183
ENSE000035038236263898362639110
ENSE000035067306263256562632745
ENSE000035170376263300562633101
ENSE000035176116263935962639467
ENSE000035186806263060162630836
ENSE000035188616263037962630505
ENSE000035284306262919462629295
ENSE000035285276263344562633514
ENSE000035312636262958862629684
ENSE000035479966262876962629012
ENSE000035502046262728962627353
ENSE000035515376262606562626165
ENSE000035723136263482162635000
ENSE000035848276262657162626684
ENSE000035870746262704862627124
ENSE000035951316263318462633271
ENSE000036234936262686062626934
ENSE000036671926262981462629957
ENSE000036824766263019762630276
ENSE000036926906262633562626447

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 99.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 150.3251 / max 1408.6541, expressed in 1825 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
120180150.00461825
1201770.3206141

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225599.35gold quality
islet of LangerhansUBERON:000000698.88gold quality
ventricular zoneUBERON:000305398.69gold quality
right ovaryUBERON:000211898.66gold quality
left ovaryUBERON:000211998.56gold quality
right lobe of thyroid glandUBERON:000111998.54gold quality
body of pancreasUBERON:000115098.49gold quality
endocervixUBERON:000045898.44gold quality
smooth muscle tissueUBERON:000113598.43gold quality
body of uterusUBERON:000985398.40gold quality
left lobe of thyroid glandUBERON:000112098.37gold quality
right uterine tubeUBERON:000130298.29gold quality
rectumUBERON:000105298.25gold quality
left uterine tubeUBERON:000130398.25gold quality
ectocervixUBERON:001224998.17gold quality
body of stomachUBERON:000116198.13gold quality
small intestine Peyer’s patchUBERON:000345498.11gold quality
right coronary arteryUBERON:000162598.05gold quality
thyroid glandUBERON:000204698.05gold quality
upper lobe of left lungUBERON:000895298.05gold quality
granulocyteCL:000009498.02gold quality
minor salivary glandUBERON:000183097.98gold quality
gall bladderUBERON:000211097.98gold quality
transverse colonUBERON:000115797.95gold quality
tibial nerveUBERON:000132397.94gold quality
upper lobe of lungUBERON:000894897.93gold quality
descending thoracic aortaUBERON:000234597.92gold quality
pituitary glandUBERON:000000797.91gold quality
stomachUBERON:000094597.89gold quality
adenohypophysisUBERON:000219697.89gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-7249no67.87
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

83 targeting GANAB, 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-4481100.0066.421669
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-6755-5P99.9565.59464
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-568099.9169.833421
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-629-3P99.8567.991875
HSA-MIR-132399.8369.892471
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-548AJ-5P99.7871.123085
HSA-MIR-548F-5P99.7871.023093
HSA-MIR-548G-5P99.7871.123085
HSA-MIR-548X-5P99.7871.123085
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-29899.6367.561916
HSA-MIR-1212299.5669.331672
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-315399.5567.592337
HSA-MIR-199A-5P99.5169.711107
HSA-MIR-199B-5P99.5169.741098
HSA-MIR-6727-3P99.4965.921333

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 10.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 18)

  • the apparent occurrence of an unusual TG 3’ splice site in intron 18 is discussed (PMID:17672918)
  • PKD3 contributes to growth and survival of prostate cancer cells (PMID:18483269)
  • reveal a novel distinction between the exocrine and endocrine cells of the pancreas and further identify PKD3 as a signaling molecule that promotes hormone-stimulated amylase secretion (PMID:19028687)
  • In males being treated for infertility, neutral alpha-glucosidase activity correlated with the percentage of sperm DNA fragmentation. (PMID:19737279)
  • Loss of the tumor suppression function of Hsp60 or GANAB contribute to aggressive cancers. (PMID:21642380)
  • these data suggest that PKD2 and PKD3 coordinate to promote prostate cancer cell invasion through p65 NF-kappaB- and HDAC1-mediated expression and activation of uPA. (PMID:22797919)
  • The high frequency of glucosidase II overexpression, which to the best of our knowledge has not been previously described, indicates its crucial roles in lung tumorigenesis and is thus a valuable biomarker (PMID:24008518)
  • Data show that similar to a knockdown of serine/threonine kinase protein kinase D3 (PKD3), treatment with this inhibitor targets all tumorigenic processes in vitro and decreases growth of primary tumors and metastasis in vivo (PMID:25852060)
  • Mutations in GANAB gene is associated with Autosomal-Dominant Polycystic Kidney and Liver Disease. (PMID:27259053)
  • used whole exome sequencing in a discovery cohort of 102 unrelated patients who were excluded for mutations in the 2 most common polycystic liver disease genes, PRKCSH and SEC63, to identify heterozygous loss-of-function mutations in 3 additional genes, ALG8, GANAB, and SEC61B. Similarly to PRKCSH and SEC63, these genes encode proteins that are integral to the protein biogenesis pathway in the endoplasmic reticulum. (PMID:28375157)
  • Case Report: GANAB mutation leading to autosomal dominant polycystic kidney disease. (PMID:28784653)
  • a novel intronic nine base pair deletion in the vicinity of the GANAB exon 24 splice donor, is reported. (PMID:29243290)
  • Our data indicate that PKD3 functions downstream of PKCiota to affect the cytokine-mediated induction of MMP1 and MMP13 in human chondrocytes. (PMID:29652915)
  • Novel GANAB variants associated with polycystic liver disease. (PMID:33097077)
  • PKD3 promotes metastasis and growth of oral squamous cell carcinoma through positive feedback regulation with PD-L1 and activation of ERK-STAT1/3-EMT signalling. (PMID:33692335)
  • Protein Kinase D3 Promotes the Reconstruction of OSCC Immune Escape Niche Via Regulating MHC-I and Immune Inhibit Molecules Expression. (PMID:34545012)
  • Glycoprotein alpha-Subunit of Glucosidase II (GIIalpha) is a novel prognostic biomarker correlated with unfavorable outcome of urothelial carcinoma. (PMID:35879690)
  • ERVW-1 Activates ATF6-Mediated Unfolded Protein Response by Decreasing GANAB in Recent-Onset Schizophrenia. (PMID:37376599)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioganabbENSDARG00000076811
danio_rerioganabaENSDARG00000076888
mus_musculusGanabENSMUSG00000071650
rattus_norvegicusGanabENSRNOG00000019724
caenorhabditis_elegansWBGENE00019895

Paralogs (6): SI (ENSG00000090402), MYORG (ENSG00000164976), GAA (ENSG00000171298), GANC (ENSG00000214013), MGAM (ENSG00000257335), MGAM2 (ENSG00000257743)

Protein

Protein identifiers

Neutral alpha-glucosidase ABQ14697 (reviewed: Q14697)

Alternative names: Alpha-glucosidase 2, Glucosidase II subunit alpha

All UniProt accessions (6): Q14697, E9PKU7, E9PNH1, E9PQ69, F5H6X6, V9HWJ0

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of glucosidase II that cleaves sequentially the 2 innermost alpha-1,3-linked glucose residues from the Glc(2)Man(9)GlcNAc(2) oligosaccharide precursor of immature glycoproteins. Required for PKD1/Polycystin-1 and PKD2/Polycystin-2 maturation and localization to the cell surface and cilia.

Subunit / interactions. Heterodimer of a catalytic alpha subunit (GANAB) and a beta subunit (PRKCSH). Binds glycosylated PTPRC.

Subcellular location. Endoplasmic reticulum. Golgi apparatus. Melanosome.

Tissue specificity. Detected in placenta. Isoform 1 and isoform 2 are expressed in the kidney and liver.

Disease relevance. Polycystic kidney disease 3 with or without polycystic liver disease (PKD3) [MIM:600666] A form of polycystic kidney disease, a disorder characterized by progressive formation and enlargement of cysts in both kidneys, typically leading to end-stage renal disease in adult life. Cysts also occur in other organs, particularly the liver. PKD3 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry. GANAB variations may act as a disease modifier in autosomal dominant polycystic liver disease in patients who have causative mutations in other genes, such as PKHD1 or ALG8.

Activity regulation. Inhibited by deoxynojirimycin.

Pathway. Glycan metabolism; N-glycan metabolism.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the glycosyl hydrolase 31 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q14697-11yes
Q14697-22
Q14697-33

RefSeq proteins (9): NP_001265121, NP_001265122, NP_001265123, NP_001316151, NP_001316152, NP_001316153, NP_001316154, NP_938148, NP_938149 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000322Glyco_hydro_31_TIMDomain
IPR011013Gal_mutarotase_sf_domHomologous_superfamily
IPR013780Glyco_hydro_bHomologous_superfamily
IPR017853GH_hydrolase_sfHomologous_superfamily
IPR025887Glyco_hydro_31_N_domDomain
IPR030458Glyco_hydro_31_ASActive_site
IPR030459Glyco_hydro_31_CSConserved_site
IPR048395Glyco_hydro_31_CDomain

Pfam: PF01055, PF13802, PF21365

Enzyme classification (BRENDA):

  • EC 3.2.1.207 — mannosyl-oligosaccharide alpha-1,3-glucosidase (BRENDA: 26 organisms, 73 substrates, 66 inhibitors, 27 Km, 5 kcat entries)

Substrate kinetics (BRENDA)

14 substrates with measured Km, best-characterized 14. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
MALTOSE0.43–57.74
P-NITROPHENYL ALPHA-D-GLUCOPYRANOSIDE0.78–4814
4-NITROPHENYL ALPHA-D-GLUCOPYRANOSIDE2.2–2.823
P-NITROPHENYL-ALPHA-D-GLUCOPYRANOSIDE0.5–0.923
4-METHYLUMBELLIFERYL ALPHA-D-GLUCOPYRANOSIDE0.013–0.0192
4-METHYLUMBELLIFERYL-ALPHA-D-GLUCOPYRANOSIDE0.00031
4-METHYLUMBELLIFERYL-ALPHA-D-GLUCOSIDE0.05521
4-METHYLUMBELLYFERYL ALPHA-D-GLUCOPYRANOSIDE0.0551
MALTOHEXAOSE15.31
MALTOTRIOSE26.71
N-[[2-CARBOXY-5-(4-METHOXYPHENYL)THIOPHEN-3-YL]C0.491
NIGEROSE2.131
P-NITROPHENYL-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE0.761
SUCROSE15.31

Catalyzed reactions (Rhea), 2 shown:

  • N(4)-(alpha-D-Glc-(1->3)-alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] + H2O = N(4)-(alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] + beta-D-glucose (RHEA:55996)
  • N(4)-(alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] + H2O = N(4)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 9A1,2,3B1,2,3) + beta-D-glucose (RHEA:56000)

UniProt features (125 total): strand 54, helix 23, sequence variant 15, turn 13, binding site 4, splice variant 3, disulfide bond 2, sequence conflict 2, active site 2, signal peptide 1, chain 1, modified residue 1, glycosylation site 1, region of interest 1, compositionally biased region 1, mutagenesis site 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8D43ELECTRON MICROSCOPY2.88
8EMRELECTRON MICROSCOPY2.92

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q14697-F193.430.90

Functional residue map

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

Catalytic / active sites (2): 542 (nucleophile); 618 (proton donor)

Ligand- & substrate-binding residues (4): 283; 429; 602; 676

Post-translational modifications (1): 52

Disulfide bonds (2): 41–47, 633–644

Glycosylation sites (1): 97

Mutagenesis-validated functional residues (1):

PositionPhenotype
542loss of activity.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-532668N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-HSA-901042Calnexin/calreticulin cycle
R-HSA-9683686Maturation of spike protein
R-HSA-9694548Maturation of spike protein
R-HSA-9768727Regulation of CDH1 posttranslational processing and trafficking to plasma membrane

MSigDB gene sets: 266 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GGGACCA_MIR133A_MIR133B, GOBP_N_GLYCAN_PROCESSING, GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, CGGAARNGGCNG_UNKNOWN, MORF_UBE2I, KEGG_N_GLYCAN_BIOSYNTHESIS, MORF_HDAC1, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, TCGATGG_MIR213, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP, WANG_LMO4_TARGETS_DN, MORF_CTBP1, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS

GO Biological Process (2): carbohydrate metabolic process (GO:0005975), N-glycan processing (GO:0006491)

GO Molecular Function (10): RNA binding (GO:0003723), carbohydrate binding (GO:0030246), glucan 1,3-alpha-glucosidase activity (GO:0033919), alpha-glucosidase activity (GO:0090599), Glc2Man9GlcNAc2 oligosaccharide glucosidase activity (GO:0106407), catalytic activity (GO:0003824), hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553), protein binding (GO:0005515), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798)

GO Cellular Component (8): endoplasmic reticulum (GO:0005783), endoplasmic reticulum lumen (GO:0005788), Golgi apparatus (GO:0005794), membrane (GO:0016020), glucosidase II complex (GO:0017177), melanosome (GO:0042470), intracellular membrane-bounded organelle (GO:0043231), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Asparagine N-linked glycosylation1
N-glycan trimming in the ER and Calnexin/Calreticulin cycle1
Translation of Structural Proteins1
Regulation of CDH1 Expression and Function1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
alpha-glucosidase activity2
cytoplasm2
endomembrane system2
intracellular membrane-bounded organelle2
primary metabolic process1
protein N-linked glycosylation1
glycoprotein biosynthetic process1
nucleic acid binding1
glucosidase activity1
molecular_function1
hydrolase activity, acting on glycosyl bonds1
catalytic activity1
hydrolase activity1
endoplasmic reticulum1
intracellular organelle lumen1
cellular anatomical structure1
endoplasmic reticulum protein-containing complex1
glucosidase complex1
pigment granule1
intracellular anatomical structure1
membrane-bounded organelle1
intracellular organelle1
extracellular vesicle1

Protein interactions and networks

STRING

3104 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GANABMOGSQ13724968
GANABPRKCSHP14314934
GANABALG8Q9BVK2805
GANABDNAJB11Q9UBS4768
GANABHYOU1Q9Y4L1755
GANABHSPA5P11021712
GANABPDIA3P30101700
GANABUGGT1Q9NYU2690
GANABSEC63Q9UGP8651
GANABSEC61BP38390649
GANABHSP90B1P14625649
GANABCALRP27797635
GANABPLA2G2AP14555621
GANABPKD1P98161613
GANABPLA2G2DQ9UNK4610

IntAct

196 interactions, top by confidence:

ABTypeScore
HSPA8GAKpsi-mi:“MI:0914”(association)0.760
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
NCBP2KPNA3psi-mi:“MI:0914”(association)0.640
CRIPTOAIPpsi-mi:“MI:0914”(association)0.640
CFTRHAX1psi-mi:“MI:0914”(association)0.610
IGF1RPIK3R2psi-mi:“MI:2364”(proximity)0.590
ADAMTS4MANBApsi-mi:“MI:0914”(association)0.530
NPTNTNPO2psi-mi:“MI:0914”(association)0.530
COL1A1GOLIM4psi-mi:“MI:0914”(association)0.500
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480
sseJAGPSpsi-mi:“MI:0914”(association)0.460
envPSMD11psi-mi:“MI:0914”(association)0.460
envAPPpsi-mi:“MI:0914”(association)0.460
envPGRMC1psi-mi:“MI:0914”(association)0.460
ZwintNDC80psi-mi:“MI:0915”(physical association)0.400
TK2psi-mi:“MI:0915”(physical association)0.400

BioGRID (517): GANAB (Affinity Capture-MS), GANAB (Affinity Capture-MS), GANAB (Affinity Capture-MS), GANAB (Affinity Capture-MS), MOGS (Co-fractionation), MRPL9 (Co-fractionation), UQCRC2 (Co-fractionation), GANAB (Affinity Capture-MS), GANAB (Proximity Label-MS), GANAB (Proximity Label-MS), GANAB (Proximity Label-MS), GANAB (Proximity Label-MS), GANAB (Affinity Capture-MS), GANAB (Affinity Capture-MS), GANAB (Affinity Capture-MS)

ESM2 similar proteins: A0JNU3, A6QNR0, O18835, O35632, O77695, O88202, O97524, P04066, P06760, P06865, P07686, P08236, P10253, P12265, P16444, P17164, P22412, P29416, P31429, P31430, P43477, P48300, P54802, P70699, P79403, Q0V8R6, Q12891, Q14697, Q3SZM7, Q3U4H6, Q4FAT7, Q4QR99, Q4R4N7, Q5R5N6, Q5R7A9, Q5RC84, Q5RFI5, Q60HF8, Q641X3, Q6AYS4

Diamond homologs: B9F676, D0KQM8, F4J6T7, O04893, O04931, O43451, P07768, P0CD66, P10253, P14410, P23739, P38138, P70699, P79403, Q12558, Q14697, Q43763, Q4R4N7, Q5R7A9, Q653V7, Q6P7A9, Q8BHN3, Q8BVW0, Q8TET4, Q92442, Q94502, Q9BE70, Q9F234, Q9FN05, Q9MYM4, Q9US55, Q09901, Q9P999, A1CNK4, A1D1E6, B0XNL6, B8MZ41, D4B0X3, O00906, O62653

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic18
Likely pathogenic33
Uncertain significance294
Likely benign170
Benign32

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1711179NM_198334.3(GANAB):c.2516C>T (p.Thr839Ile)Pathogenic
2050292NM_198334.3(GANAB):c.499_500del (p.Leu167fs)Pathogenic
253129NM_198334.3(GANAB):c.1848_1849del (p.Asp618fs)Pathogenic
253130NM_198334.3(GANAB):c.1148C>G (p.Thr383Arg)Pathogenic
253131NM_198334.3(GANAB):c.2624+2_2624+7delPathogenic
2691267NM_198334.3(GANAB):c.1936+1delPathogenic
2700204NM_198334.3(GANAB):c.2280_2281del (p.Gly761fs)Pathogenic
2783444NM_198334.3(GANAB):c.755del (p.Gly252fs)Pathogenic
3236796NM_198334.3(GANAB):c.1310_1320del (p.Arg437fs)Pathogenic
3254987NM_198334.3(GANAB):c.1495G>T (p.Glu499Ter)Pathogenic
492969NM_198334.3(GANAB):c.2725+4_2725+12delPathogenic
590347NM_198334.3(GANAB):c.11_16del (p.Val4_Ala5del)Pathogenic
590348NM_198334.3(GANAB):c.621del (p.Asp207fs)Pathogenic
590349NM_198334.3(GANAB):c.1769G>C (p.Arg590Pro)Pathogenic
590350NM_198334.3(GANAB):c.1936+1G>CPathogenic
590352NM_198334.3(GANAB):c.2590C>T (p.Arg864Ter)Pathogenic
620175NM_198334.3(GANAB):c.181C>T (p.Arg61Ter)Pathogenic
810838NC_000011.10:g.62628412_62655064delPathogenic
1691315NM_198334.3(GANAB):c.560+444A>CLikely pathogenic
1803160NM_198334.3(GANAB):c.1429T>C (p.Tyr477His)Likely pathogenic
2505230NM_198334.3(GANAB):c.517C>T (p.Arg173Ter)Likely pathogenic
253132NM_198334.3(GANAB):c.2449C>T (p.Arg817Trp)Likely pathogenic
2572928NM_198334.3(GANAB):c.2110C>T (p.Arg704Ter)Likely pathogenic
2575050NM_198334.3(GANAB):c.677G>A (p.Trp226Ter)Likely pathogenic
2575052NM_198334.3(GANAB):c.644_645del (p.Gln215fs)Likely pathogenic
3057233NM_198334.3(GANAB):c.1502G>A (p.Trp501Ter)Likely pathogenic
3068388NM_198334.3(GANAB):c.12_38+2delLikely pathogenic
3236803NM_198334.3(GANAB):c.174_175del (p.Pro59fs)Likely pathogenic
3256692NM_198334.3(GANAB):c.842dup (p.Asn281fs)Likely pathogenic
3599837NM_198334.3(GANAB):c.2496_2502del (p.Ser835fs)Likely pathogenic

SpliceAI

3336 predictions. Top by Δscore:

VariantEffectΔscore
11:62625922:ATCC:Aacceptor_loss1.0000
11:62625923:TC:Tacceptor_gain1.0000
11:62625924:CC:Cacceptor_gain1.0000
11:62625925:C:CCacceptor_gain1.0000
11:62626061:TCAC:Tdonor_loss1.0000
11:62626062:CACC:Cdonor_loss1.0000
11:62626063:A:ACdonor_gain1.0000
11:62626063:AC:Adonor_gain1.0000
11:62626063:ACCT:Adonor_loss1.0000
11:62626064:C:CAdonor_loss1.0000
11:62626064:C:CCdonor_gain1.0000
11:62626064:CC:Cdonor_gain1.0000
11:62626064:CCT:Cdonor_gain1.0000
11:62626064:CCTT:Cdonor_gain1.0000
11:62626161:CTGAG:Cacceptor_gain1.0000
11:62626162:TGAG:Tacceptor_gain1.0000
11:62626163:GAG:Gacceptor_gain1.0000
11:62626164:AG:Aacceptor_gain1.0000
11:62626166:C:CCacceptor_gain1.0000
11:62626172:A:ACacceptor_gain1.0000
11:62626172:A:Cacceptor_gain1.0000
11:62626175:G:Cacceptor_gain1.0000
11:62626175:G:GCacceptor_gain1.0000
11:62626182:C:CTacceptor_gain1.0000
11:62626190:C:CTacceptor_gain1.0000
11:62626193:C:CTacceptor_gain1.0000
11:62626194:A:Tacceptor_gain1.0000
11:62626329:CATTA:Cdonor_loss1.0000
11:62626331:TTA:Tdonor_loss1.0000
11:62626332:TA:Tdonor_loss1.0000

AlphaMissense

6149 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:62628996:G:CF651L1.000
11:62628996:G:TF651L1.000
11:62628998:A:GF651L1.000
11:62629277:T:AD618V1.000
11:62629277:T:GD618A1.000
11:62629287:A:GW615R1.000
11:62629287:A:TW615R1.000
11:62628923:G:CH676D0.999
11:62629277:T:CD618G0.999
11:62629278:C:GD618H0.999
11:62629285:C:AW615C0.999
11:62629285:C:GW615C0.999
11:62629617:C:AR602M0.999
11:62629904:G:CF549L0.999
11:62629904:G:TF549L0.999
11:62629906:A:GF549L0.999
11:62629926:T:AD542V0.999
11:62629933:A:GW540R0.999
11:62629933:A:TW540R0.999
11:62630383:C:AW503C0.999
11:62630383:C:GW503C0.999
11:62630385:A:GW503R0.999
11:62630385:A:TW503R0.999
11:62630701:T:AD429V0.999
11:62630786:A:GW401R0.999
11:62630786:A:TW401R0.999
11:62631117:A:GW355R0.999
11:62631117:A:TW355R0.999
11:62632713:T:AD283V0.999
11:62628997:A:GF651S0.998

dbSNP variants (sampled 300 via entrez): RS1000012695 (11:62635200 T>A), RS1000088195 (11:62642367 T>G), RS1000153104 (11:62627631 C>T), RS1000221761 (11:62637981 T>C), RS1000344692 (11:62632182 C>T), RS1000686133 (11:62643445 C>A,G), RS1000728814 (11:62643651 T>C), RS1000777541 (11:62631877 C>A), RS1000918508 (11:62643916 C>G), RS1000928320 (11:62633629 G>A,T), RS1000972057 (11:62643639 C>T), RS1001063199 (11:62638630 G>A), RS1001191042 (11:62637850 C>G), RS1001353340 (11:62626813 G>C,T), RS1001548701 (11:62632265 C>T)

Disease associations

OMIM: gene MIM:104160 | disease phenotypes: MIM:600666, MIM:174050, MIM:620369

GenCC curated gene-disease

DiseaseClassificationInheritance
polycystic kidney disease 3 with or without polycystic liver diseaseDefinitiveAutosomal dominant
autosomal dominant polycystic kidney diseaseSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
polycystic kidney disease 3 with or without polycystic liver diseaseDefinitiveAD

Mondo (7): polycystic kidney disease 3 with or without polycystic liver disease (MONDO:0010916), autosomal dominant polycystic liver disease (MONDO:0000447), cystic kidney disease (MONDO:0002473), biliary tract disorder (MONDO:0004868), congenital myopathy 22B, severe fetal (MONDO:0957265), autosomal dominant polycystic kidney disease (MONDO:0004691), chronic kidney disease (MONDO:0005300)

Orphanet (2): Isolated polycystic liver disease (Orphanet:2924), Autosomal dominant polycystic kidney disease (Orphanet:730)

HPO phenotypes

33 total (30 of 33 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000010Recurrent urinary tract infections
HP:0000083Renal insufficiency
HP:0000105Enlarged kidney
HP:0000107Renal cyst
HP:0000113Polycystic kidney dysplasia
HP:0000790Hematuria
HP:0000791Uric acid nephrolithiasis
HP:0000822Hypertension
HP:0001407Hepatic cysts
HP:0001410Decreased liver function
HP:0001634Mitral valve prolapse
HP:0001737Pancreatic cysts
HP:0002616Aortic root aneurysm
HP:0003259Elevated circulating creatinine concentration
HP:0003584Late onset
HP:0003596Middle age onset
HP:0003621Juvenile onset
HP:0003774Stage 5 chronic kidney disease
HP:0004944Dilatation of the cerebral artery
HP:0006557Polycystic liver disease
HP:0008672Calcium oxalate nephrolithiasis
HP:0011004Abnormal systemic arterial morphology
HP:0011462Young adult onset
HP:0011760Pituitary growth hormone cell adenoma
HP:0012207Reduced sperm motility
HP:0012213Decreased glomerular filtration rate
HP:0012330Pyelonephritis
HP:0012591Abnormal urinary electrolyte concentration
HP:0012592Albuminuria

GWAS associations

9 associations (top):

StudyTraitp-value
GCST005956_12Waist-to-hip ratio adjusted for BMI2.000000e-06
GCST005956_2Waist-to-hip ratio adjusted for BMI1.000000e-08
GCST005962_37Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)5.000000e-07
GCST005962_51Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)1.000000e-07
GCST90020024_382A body shape index2.000000e-11
GCST90020025_947Waist-to-hip ratio adjusted for BMI1.000000e-16
GCST90020026_778Hip index5.000000e-08
GCST90020027_1466Waist-hip index4.000000e-17
GCST90020029_314Waist circumference adjusted for body mass index2.000000e-10

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (4)

DescriptorNameTree numbers
D001660Biliary Tract DiseasesC06.130
D052177Kidney Diseases, CysticC12.050.351.968.419.403; C12.200.777.419.403; C12.950.419.403
D007676Kidney Failure, ChronicC12.050.351.968.419.780.750.500; C12.200.777.419.780.750.500; C12.950.419.780.750.500; C23.550.291.500.906.500
D016891Polycystic Kidney, Autosomal DominantC12.050.351.968.419.403.875.500; C12.200.777.419.403.875.500; C12.950.419.403.875.500; C16.131.077.717.500; C16.320.184.625.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2519 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 4,739 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL307429DUVOGLUSTAT24,739

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

ChEMBL bioactivities

10 potent at pChembl≥5 of 21 total, top 10 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.85Ki14nMDUVOGLUSTAT
7.82Ki15nMCHEMBL421040
7.39Kd40.23nMCHEMBL5653589
7.39ED5040.23nMCHEMBL5653589
6.80Ki160nMDUVOGLUSTAT
5.89IC501300nMDUVOGLUSTAT
5.52Ki3000nMCHEMBL108656
5.39Kd4094nMCHEMBL3752910
5.39ED504094nMCHEMBL3752910
5.10Ki8000nMCHEMBL111326

PubChem BioAssay actives

3 with measured affinity, of 70 total; 3 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148412: Binding affinity to human GANAB incubated for 45 mins by Kinobead based pull down assaykd0.0402uM
(2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol37439: Tested for competitive inhibition of endoplasmic reticulum alpha-glucosidase II.ic501.3000uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148412: Binding affinity to human GANAB incubated for 45 mins by Kinobead based pull down assaykd4.0937uM

CTD chemical–gene interactions

58 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression2
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance2
Acroleinaffects cotreatment, increases oxidation, increases abundance2
Benzo(a)pyreneaffects methylation2
Ozoneaffects cotreatment, increases oxidation, increases abundance2
Valproic Acidaffects cotreatment, increases expression, decreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
bisphenol Fincreases expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
deoxynivalenoldecreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, decreases expression1
tetrahydropalmatinedecreases expression1
sodium arsenitedecreases expression1
cobaltous chloridedecreases expression1
benzo(e)pyreneincreases methylation1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
aflatoxin B2increases methylation1
epigallocatechin gallatedecreases expression1
perfluorooctane sulfonic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
bisphenol Bincreases expression1
bisphenol Sincreases expression1
LDN 193189affects cotreatment, increases expression1
bisphenol AFincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Bortezomibdecreases expression1
Arsenic Trioxideincreases expression1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Atrazineincreases expression1

ChEMBL screening assays

38 unique, capped per target: 32 binding, 6 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1685139BindingInhibition of endoplasmic reticulum alpha-glucosidase 2 in human HL-60 cells assessed as free oligosaccharide level at 50 uM after 24 hrsSynthesis of N-alkylated noeurostegines and evaluation of their potential as treatment for Gaucher’s disease. — Bioorg Med Chem Lett
CHEMBL818494FunctionalCompetitive Inhibition constant on rice alpha Mannosidase; MI=Moderate InhibitionSynthesis and biological activity of C-6 modified derivatives of the glucosidase inhibitor 1-deoxynojirimycin. — Bioorg Med Chem Lett

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D1MQAbcam K-562 GANAB KOCancer cell lineFemale
CVCL_D2JAAbcam Raji GANAB KOCancer cell lineMale
CVCL_SP54HAP1 GANAB (-) 1Cancer cell lineMale
CVCL_SP55HAP1 GANAB (-) 2Cancer cell lineMale
CVCL_UQ57Abcam Jurkat GANAB KOCancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00414440PHASE4COMPLETEDEfficacy, Safety and Tolerability of Everolimus in Preventing End-stage Renal Disease in Patients With Autosomal Dominant Polycystic Kidney Disease
NCT03273413PHASE4ACTIVE_NOT_RECRUITINGStatin Therapy in Patients With Early Stage ADPKD
NCT03949894PHASE4COMPLETEDEvaluating the Safety and effectivenesS in Adult KorEaN Patients Treated With Tolvaptan for Management of Autosomal domInAnt poLycystic Kidney Disease
NCT00309283PHASE3COMPLETEDSomatostatin in Polycystic Kidney: a Long-term Three Year Follow up Study
NCT00346918PHASE3COMPLETEDSirolimus (Rapamune®) for Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT00428948PHASE3COMPLETEDTolvaptan Phase 3 Efficacy and Safety Study in Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT01022424PHASE3COMPLETEDA Long-term Administration Study of OPC-41061 in Patients With Autosomal Dominant Polycystic Kidney Disease (ADPKD) (2) [Extension of Study 156-05-002]
NCT01214421PHASE3COMPLETEDTolvaptan Extension Study in Participants With ADPKD
NCT01377246PHASE3COMPLETEDSomatostatin In Patients With Autosomal Dominant Polycystic Kidney Disease And Moderate To Severe Renal Insufficiency
NCT01616927PHASE3UNKNOWNStudy of Lanreotide to Treat Polycystic Kidney Disease
NCT01853553PHASE3COMPLETEDMineralocorticoid Antagonism and Endothelial Dysfunction in Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT02115659PHASE3UNKNOWNTriptolide-Containing Formulation as Treatment for Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT02134899PHASE3COMPLETEDThe Efficacy of Everolimus in Reducing Total Native Kidney Volume in Polycystic Kidney Disease Transplanted Recipients
NCT02160145PHASE3COMPLETEDEfficacy and Safety of Tolvaptan in Subjects With Chronic Kidney Disease Between Late Stage 2 to Early Stage 4 Due to Autosomal Dominant Polycystic Kidney Disease
NCT02964273PHASE3COMPLETEDSafety, Pharmacokinetics, Tolerability and Efficacy of Tolvaptan in Children and Adolescents With ADPKD (Autosomal Dominant Polycystic Kidney Disease)
NCT03764605PHASE3UNKNOWNMetformin vs Tolvaptan for Treatment of Autosomal Dominant Polycystic Kidney Disease
NCT03918447PHASE3TERMINATEDA Trial of Bardoxolone Methyl in Patients With ADPKD - FALCON
NCT04064346PHASE3TERMINATEDEfficacy and Safety of Lixivaptan in the Treatment of Autosomal Dominant Polycystic Kidney Disease
NCT04152837PHASE3TERMINATEDSafety of Lixivaptan in Subjects Previously Treated With Tolvaptan for Autosomal Dominant Polycystic Kidney Disease
NCT04939935PHASE3RECRUITINGImplementation of Metformin theraPy to Ease Decline of Kidney Function in Polycystic Kidney Disease (IMPEDE-PKD)
NCT05373264PHASE3RECRUITINGHYDROchlorothiazide to PROTECT Polycystic Kidney Disease Patients and Improve Their Quality of Life
NCT04705051PHASE3TERMINATEDLong-term Treatment of Autosomal Dominant Polycystic Kidney Disease (ADPKD) With Venglustat
NCT00841568PHASE2COMPLETEDA Long-term Administration Study of OPC-41061 in Patients With Autosomal Dominant Polycystic Kidney Disease (ADPKD) [Extension of Study 156-04-001]
NCT01210560PHASE2COMPLETEDDose-finding Study of New Tolvaptan Formulation in Subjects With ADPKD
NCT01336972PHASE2COMPLETEDShort-term Renal Hemodynamic Effects of Tolvaptan in Subjects With Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT01451827PHASE2COMPLETED8-Week Study of Tolvaptan Dose Forms in Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT01670110PHASE2COMPLETEDPasireotide LAR in Severe Polycystic Liver Disease
NCT01932450PHASE2UNKNOWNRadiofrequency Ablation for ADPKD Blood Pressure and Disease Progression Control
NCT02527863PHASE2COMPLETEDEffect of the Aquaretic Tolvaptan on Nitric Oxide System
NCT02616055PHASE2TERMINATEDLong-Term Treatment and Follow up of Subjects Completing 24 Months of Treatment With Tesevatinib on Study KD019-101
NCT03203642PHASE2COMPLETEDStudy of the Efficacy and Safety of Tesevatinib in Subjects With ADPKD
NCT03487913PHASE2COMPLETEDThe ELiSA Study - Evaluation of Lixivaptan in Subjects With Autosomal Dominant Polycystic Kidney Disease
NCT03541447PHASE2COMPLETEDTolvaptan-Octreotide LAR Combination in ADPKD
NCT04284657PHASE2COMPLETEDPravastatin and Alkali Therapy in Patients With Autosomal Dominant Polycystic Kidney Disease
NCT04578548PHASE2TERMINATEDA Study to Evaluate the Effects of GLPG2737 in Participants With Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT05190744PHASE2COMPLETEDProbenecid (PB) to Treat Hereditary Nephrogenic Diabetes Insipidus (NDI), ADPKD Treated With Tolvaptan, and Severely Polyuric Patients With Previous Lithium Administration
NCT05870007PHASE2ENROLLING_BY_INVITATIONAtorvastatin and Alkali Therapy in Patients With Autosomal Dominant Polycystic Kidney Disease
NCT06100133PHASE2UNKNOWNTreat Autosomal Dominant Polycystic Kidney Disease With Oral Ketone Ester?
NCT06289998PHASE2ACTIVE_NOT_RECRUITINGStudy of Tamibarotene in Patients With ADPKD
NCT06435858PHASE2RECRUITINGShort-term Effects of an SGLT2 Inhibitor on Divalent Ions in Autosomal Dominant Polycystic Kidney Disease