GALC

gene
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Summary

GALC (galactosylceramidase, HGNC:4115) is a protein-coding gene on chromosome 14q31.3, encoding Galactocerebrosidase (P54803). Hydrolyzes the galactose ester bonds of glycolipids such as galactosylceramide and galactosylsphingosine.

This gene encodes a lysosomal protein which hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Mutations in this gene have been associated with Krabbe disease, also known as globoid cell leukodystrophy. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.

Source: NCBI Gene 2581 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Krabbe disease (Definitive, ClinGen)
  • GWAS associations: 25
  • Clinical variants (ClinVar): 1,639 total — 192 pathogenic, 147 likely-pathogenic
  • Phenotypes (HPO): 133
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_000153

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4115
Approved symbolGALC
Namegalactosylceramidase
Location14q31.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000054983
Ensembl biotypeprotein_coding
OMIM606890
Entrez2581

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 8 protein_coding, 5 nonsense_mediated_decay, 3 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000261304, ENST00000393568, ENST00000393569, ENST00000474294, ENST00000477716, ENST00000544807, ENST00000554372, ENST00000554916, ENST00000555000, ENST00000555179, ENST00000555956, ENST00000556261, ENST00000556879, ENST00000557316, ENST00000557520, ENST00000622264, ENST00000872271, ENST00000921945, ENST00000950382

RefSeq mRNA: 10 — MANE Select: NM_000153 NM_000153, NM_001201401, NM_001201402, NM_001424071, NM_001424072, NM_001424073, NM_001424074, NM_001424075, NM_001424076, NM_001424077

CCDS: CCDS55936, CCDS55937, CCDS9878

Canonical transcript exons

ENST00000261304 — 17 exons

ExonStartEnd
ENSE000012204388799297087993182
ENSE000025005618793301487934878
ENSE000034829358796338487963511
ENSE000035059288794772887947878
ENSE000035342048796833587968490
ENSE000035433778793990587939981
ENSE000035513918798220587982243
ENSE000035730618798648987986602
ENSE000035740138796550587965629
ENSE000035815518794139587941558
ENSE000036109288794555387945733
ENSE000036132358798814487988207
ENSE000036317038797635887976488
ENSE000036491678794984587949931
ENSE000036741588798845587988523
ENSE000036754368798439487984533
ENSE000036788218795065987950748

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 98.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.2667 / max 711.2634, expressed in 1755 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
14439220.28981743
1443909.45931607
1443912.45441131
1443881.0666574
1443890.5868234
1443870.4098163

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
adrenal tissueUBERON:001830398.79gold quality
bronchial epithelial cellCL:000232896.74gold quality
jejunal mucosaUBERON:000039996.45gold quality
renal glomerulusUBERON:000007496.09gold quality
metanephric glomerulusUBERON:000473696.03gold quality
germinal epithelium of ovaryUBERON:000130494.81gold quality
epithelium of bronchusUBERON:000203194.49gold quality
cranial nerve IIUBERON:000094194.42gold quality
pigmented layer of retinaUBERON:000178294.31gold quality
duodenumUBERON:000211494.21gold quality
bronchusUBERON:000218594.15gold quality
trigeminal ganglionUBERON:000167593.91gold quality
inferior vagus X ganglionUBERON:000536393.88gold quality
corpus callosumUBERON:000233693.75gold quality
visceral pleuraUBERON:000240193.31gold quality
lateral globus pallidusUBERON:000247692.88gold quality
subthalamic nucleusUBERON:000190692.87gold quality
monocyteCL:000057692.28gold quality
mononuclear cellCL:000084292.18gold quality
leukocyteCL:000073891.92gold quality
superior vestibular nucleusUBERON:000722791.81gold quality
metanephrosUBERON:000008191.75gold quality
pleuraUBERON:000097791.65gold quality
dorsal root ganglionUBERON:000004491.51gold quality
spinal cordUBERON:000224091.36gold quality
endothelial cellCL:000011591.35gold quality
middle frontal gyrusUBERON:000270291.29gold quality
C1 segment of cervical spinal cordUBERON:000646991.21gold quality
substantia nigra pars reticulataUBERON:000196691.18gold quality
Brodmann (1909) area 23UBERON:001355491.13gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-CURD-122yes11.60
E-ANND-3yes11.56
E-MTAB-9067yes11.44
E-CURD-112yes10.51
E-MTAB-9801yes6.47

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

97 targeting GALC, 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-3613-3P100.0076.367965
HSA-MIR-196A-5P100.0068.16684
HSA-MIR-196B-5P100.0068.16681
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-5692A100.0074.406850
HSA-MIR-450099.9972.722367
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-314899.9775.066478
HSA-MIR-807599.9767.20962
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-60799.9773.625593
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-651-3P99.9473.485177

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 39)

  • A GALC genotype with one deleted and one polymorphic GALC activity-reducing allele can lead to enzymatic and clinical signs of LOGLD in the absence of marked GALC-PS deficiency (PMID:11814461)
  • galactocerebrosidase and galactosylcerebroside have roles in cancer cells (PMID:15657896)
  • confirm several mutations common to Japanese patients, the two most frequent being 12Del3Ins and I66M+I289V, which account for 37% of all mutant alleles (PMID:16607461)
  • Psychosine reduces apoptotic response and causes atypical cytokine production in peripheral immune cells of Krabbe patients. (PMID:17458901)
  • molecular analysis in 5 families with late onset Krabbe disease from Catania, Sicily shows that this condition is mainly due to a p.Gly41Ser substitution in the GALC gene that abolishes catalytic activity of the galactocerebrosidase enzyme (PMID:17579360)
  • This study analyzes the effects of Asp528Asn, Iso234Thr, and Leu629Arg mutations on GALC intracellular processing, secretion, uptake, and subcellular localization in mammalian cell lines. (PMID:20410102)
  • This study, reporting one of the largest genotype-phenotype analyses of the GALC gene so far performed in a European Krabbe disease cohort, revealed that the Italian GALC mutational profile differs significantly from other populations of European origin. (PMID:20886637)
  • The p.Gly41Ser mutation was associated with longer survival with Krabbe disease. A wide spectrum of late onset Krabbe leukodystrophy is found despite similar genotype. (PMID:21070211)
  • suggest that heterozygous deletions that reduce GALC activity are a novel mechanism increasing risk of POAG (PMID:22073273)
  • Higher galactocerebrosidase activity is predictive of later symptom onset times but does not predict survival after symptom onset when controlling for the logarithm of age at onset. (PMID:23044012)
  • GALC mutation is associated with Krabbe disease. (PMID:23276707)
  • study identified 4 novel mutations of the GALC gene in 2 unrelated Chinese families with Krabbe disease: one insertion mutation, c.1836_1837insT, one nonsense mutation, c.599C>A (p.S200X),one deletion mutation, c.1911 1_1911 5delGTAAG and one missense mutation, c.2041G>A (PMID:23462331)
  • Itis an exoglycosidase that catalyzes the hydrolysis of terminal beta-linked galactose residues and its deficiencies or mutation cause llysosomal diseases. (review) (PMID:23649392)
  • Structural snapshots illustrate the catalytic cycle of beta-galactocerebrosidase, the defective enzyme in Krabbe disease. (PMID:24297913)
  • Genetic variants near IREB2 and GALC likely contribute to genetic susceptibility to PAE associated with COPD. (PMID:25101718)
  • We demonstrated that a heterozygous GALC deletion does not play a significant role in the pathogenesis of normal tension glaucoma in a representative clinic-based population of South Koreans, unlike whites. (PMID:25943734)
  • GALC was downregulated by promoter hypermethylation and contributed to the pathogenesis of EBV-associated nasopharyngeal carcinoma (PMID:26178533)
  • promoter hypermethylation contributed to down-regulation of GALC Gene, implicating epigenetic inactivation of GALC may play a role in tumorigenesis of cancer. (PMID:26617822)
  • Mutations in GALC cause late-onset Krabbe disease with predominant cerebellar ataxia (PMID:26915362)
  • Enzyme activities (acid alpha-glucosidase (GAA), galactocerebrosidase (GALC), glucocerebrosidase (GBA), alpha-galactosidase A (GLA), alpha-iduronidase (IDUA) and sphingomyeline phosphodiesterase-1 (SMPD-1)) were measured on ~43,000 de-identified dried blood spot (DBS) punches, and screen positive samples were submitted for DNA sequencing to obtain genotype confirmation of disease risk (PMID:27238910)
  • Case Report: compound GALC heterozygosity in a boy with infantile Krabbe disease with severe clinical course. (PMID:27442402)
  • This review illustrated The Krabbe’s disease is caused by mutation in the enzyme Beta-galactocerebrosidase. (PMID:27638582)
  • This is the largest expression study of GALC variants/mutations found in Newborn screening and confirmed KD cases. (PMID:27638593)
  • we showed for the first time the specific alteration of beta-Galctosidase (Gal), beta-Galactosylcerebrosidase (GALC) in MCI patients. It is notable that in above peripheral biological samples the lysosomes are more sensitive to AD cellular metabolic alteration when compared to levels of Abeta-peptide or Tau proteins, similar in both AD groups analyzed (PMID:28825628)
  • rs17203398 associated with mucous membrane pemphigoid (PMID:29136295)
  • The authors present the structure of a glycosphingolipid-processing complex, revealing how SapA and GALC form a heterotetramer with an open channel connecting the enzyme active site to the SapA hydrophobic cavity. (PMID:29323104)
  • Results show for the first time that during normal aging, psychosine metabolism is progressively dysfunctional, leading to its accumulation in the aging brain, especially in regions vulnerable to degeneration in Parkinson’s disease (PD). These results underline the possibility that defects in the metabolism mediated by changes in GALC activity modify the risk of developing alpha-synuclein pathology in vulnerable patients. (PMID:29481565)
  • EMT phenotypes and GALC expression of CTCs are correlated with cancer metastasis and therapeutic outcomes, suggesting them to be potential markers for the prognosis of NSCLC. (PMID:29758927)
  • The present study describes two GALC mutations shared by two Chinese siblings with juvenile-onset of Krabbe disease (PMID:31185936)
  • Self-association of beta-galactocerebrosidase (human GALC)decreases as the concentration of sodium chloride increases from 50 to 500 mM. This indicates that ionic interactions are involved in the association. These results indicate that GALC has the highest tendency for oligomerization at physiological ionic strength and pH (lysosomal lumen). (PMID:31869371)
  • Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe’s disease. (PMID:32186243)
  • This study generated information on the recessive allele frequency dynamics of GALC gene across 15 global populations. (PMID:32304783)
  • beta-Galactosylceramidase Promotes Melanoma Growth via Modulation of Ceramide Metabolism. (PMID:32998995)
  • Brainstem development requires galactosylceramidase and is critical for pathogenesis in a model of Krabbe disease. (PMID:33097716)
  • Two Cases of Female Chinese Adult-Onset Krabbe Disease with One Novel Mutation and a Review of Literature. (PMID:33190188)
  • beta-Galactosidase is a target enzyme for detecting peritoneal metastasis of gastric cancer. (PMID:34021168)
  • Galactosylceramidase deficiency and pathological abnormalities in cerebral white matter of Krabbe disease. (PMID:36113749)
  • GALC variants affect galactosylceramidase enzymatic activity and risk of Parkinson’s disease. (PMID:36370000)
  • A novel mutation in the GALC gene causes Krabbe disease accompanied with extensive Mongolian spots in a consanguineous family. (PMID:36920572)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriogalcbENSDARG00000016474
danio_reriogalcaENSDARG00000037064
mus_musculusGalcENSMUSG00000021003
rattus_norvegicusGalcENSRNOG00000003759
caenorhabditis_elegansWBGENE00016207

Protein

Protein identifiers

GalactocerebrosidaseP54803 (reviewed: P54803)

Alternative names: Galactocerebroside beta-galactosidase, Galactosylceramidase, Galactosylceramide beta-galactosidase

All UniProt accessions (8): A0A087WX10, A0A0A0MQV0, P54803, G3V255, G3V4M2, G3V5E8, H0YJG8, H0YJV6

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolyzes the galactose ester bonds of glycolipids such as galactosylceramide and galactosylsphingosine. Enzyme with very low activity responsible for the lysosomal catabolism of galactosylceramide, a major lipid in myelin, kidney and epithelial cells of small intestine and colon.

Subcellular location. Lysosome.

Tissue specificity. Detected in urine. Detected in testis, brain and placenta (at protein level). Detected in kidney and liver.

Disease relevance. Krabbe disease (KRB) [MIM:245200] An autosomal recessive disorder characterized by insufficient catabolism of several galactolipids that are important for normal myelin production. Four clinical forms are recognized. The infantile form accounts for 90% of cases. It manifests before six months of age with irritability, spasticity, arrest of motor and mental development, and bouts of temperature elevation without infection. This is followed by myoclonic jerks of arms and legs, oposthotonus, hypertonic fits, and mental regression, which progresses to a severe decerebrate condition with no voluntary movements and death from respiratory infections or cerebral hyperpyrexia before 2 years of age. Cases with later onset present with unexplained blindness, weakness and sensorimotor peripheral neuropathy, mental deterioration and death. The disease is caused by variants affecting the gene represented in this entry.

Polymorphism. Polymorphic amino-acid changes are responsible for the wide range of catalytic activities found in the general population.

Similarity. Belongs to the glycosyl hydrolase 59 family.

Isoforms (4)

UniProt IDNamesCanonical?
P54803-11yes
P54803-33
P54803-44
P54803-55

RefSeq proteins (10): NP_000144, NP_001188330, NP_001188331, NP_001411000, NP_001411001, NP_001411002, NP_001411003, NP_001411004, NP_001411005, NP_001411006 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001286Glyco_hydro_59Family
IPR013785Aldolase_TIMHomologous_superfamily
IPR017853GH_hydrolase_sfHomologous_superfamily
IPR035394Glyco_hydro_59_domDomain
IPR049161GH59_catDomain
IPR049162GH59_CDomain

Pfam: PF02057, PF17387, PF21708

Enzyme classification (BRENDA):

  • EC 3.2.1.46 — galactosylceramidase (BRENDA: 5 organisms, 18 substrates, 19 inhibitors, 14 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
6-HEXADECANOYLAMINO-4-METHYLBELLIFERYL-BETA-D-GA0.017–0.155
GALACTOSYLCERAMIDE0.02–0.24
GALACTOCEREBROSIDE0.005–0.0252
GALACTOSYLSPHINGOSINE0.11–0.672
4-METHYLUMBELLIFERYL-BETA-D-GALACTOPYRANOSIDE0.471

Catalyzed reactions (Rhea), 3 shown:

  • a beta-D-galactosyl-(1<->1’)-N-acylsphing-4-enine + H2O = an N-acylsphing-4-enine + D-galactose (RHEA:14297)
  • a D-galactosylceramide + H2O = an N-acyl-sphingoid base + D-galactose (RHEA:43412)
  • beta-D-galactosyl-(1<->1)-sphing-4-enine + H2O = sphing-4-enine + D-galactose (RHEA:43908)

UniProt features (74 total): sequence variant 51, glycosylation site 6, splice variant 4, binding site 4, sequence conflict 4, active site 2, signal peptide 1, chain 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P54803-F194.560.92

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): 198 (proton donor/acceptor); 274 (nucleophile)

Ligand- & substrate-binding residues (4): 109; 151; 197; 396

Disulfide bonds (1): 287–394

Glycosylation sites (6): 403, 556, 559, 602, 143, 379

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9840310Glycosphingolipid catabolism

MSigDB gene sets: 490 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, GOBP_CERAMIDE_CATABOLIC_PROCESS, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP, KEGG_LYSOSOME, GOBP_MEMBRANE_LIPID_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, SHEPARD_BMYB_MORPHOLINO_DN, MAHAJAN_RESPONSE_TO_IL1A_DN, GOBP_GLYCOLIPID_CATABOLIC_PROCESS, GOBP_SPHINGOLIPID_METABOLIC_PROCESS, KOYAMA_SEMA3B_TARGETS_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4

GO Biological Process (6): galactosylceramide catabolic process (GO:0006683), myelination (GO:0042552), glycosphingolipid catabolic process (GO:0046479), lipid metabolic process (GO:0006629), sphingolipid metabolic process (GO:0006665), lipid catabolic process (GO:0016042)

GO Molecular Function (3): galactosylceramidase activity (GO:0004336), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798)

GO Cellular Component (3): lysosome (GO:0005764), membrane (GO:0016020), lysosomal lumen (GO:0043202)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Glycosphingolipid metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lipid metabolic process2
galactosylceramide metabolic process1
galactolipid catabolic process1
glycosylceramide catabolic process1
axon ensheathment1
glycosphingolipid metabolic process1
glycolipid catabolic process1
sphingolipid catabolic process1
primary metabolic process1
catabolic process1
glycosylceramidase activity1
catalytic activity1
hydrolase activity1
lytic vacuole1
cellular anatomical structure1
lysosome1
vacuolar lumen1

Protein interactions and networks

STRING

1066 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GALCARSAP15289859
GALCPSAPP07292851
GALCASAH1Q13510835
GALCGLB1P16278821
GALCMBPP02686814
GALCGBA1P04062796
GALCGLAP06280771
GALCCNPP09543758
GALCSMPD1P17405729
GALCGFAPP14136702
GALCUGT8Q16880694
GALCOLIG2Q13516650
GALCNESP48681621
GALCOLIG1Q8TAK6615
GALCPDGFRAP16234613

IntAct

35 interactions, top by confidence:

ABTypeScore
ESS2ACADSpsi-mi:“MI:0914”(association)0.640
CLEC11AVWA8psi-mi:“MI:0914”(association)0.530
TMEM51WWP2psi-mi:“MI:0914”(association)0.530
IER2KPNA3psi-mi:“MI:0914”(association)0.530
EEF2KMTBCAT2psi-mi:“MI:0914”(association)0.530
CST7CTSLpsi-mi:“MI:0914”(association)0.530
ESS2HSPA8psi-mi:“MI:0914”(association)0.530
GTF2H2CERCC3psi-mi:“MI:0914”(association)0.530
NEDD1CEP290psi-mi:“MI:0914”(association)0.480
GALCH1-2psi-mi:“MI:0915”(physical association)0.400
NCOA5GALCpsi-mi:“MI:0915”(physical association)0.400
ECI2ARID1Apsi-mi:“MI:0914”(association)0.350
ECH1MCRIP1psi-mi:“MI:0914”(association)0.350
ECI2PDLIM1psi-mi:“MI:0914”(association)0.350
ECH1A2ML1psi-mi:“MI:0914”(association)0.350
APBB1SSPOPpsi-mi:“MI:0914”(association)0.350
HLA-Cpsi-mi:“MI:0914”(association)0.350
OS9GXYLT2psi-mi:“MI:0914”(association)0.350
PNMA2TARS3psi-mi:“MI:0914”(association)0.350
IGF2RMANBApsi-mi:“MI:0914”(association)0.350
CNKSR1TRIM24psi-mi:“MI:0914”(association)0.350
TRMT11NARS1psi-mi:“MI:0914”(association)0.350
IKZF1MTA2psi-mi:“MI:0914”(association)0.350
DNAJC17SYF2psi-mi:“MI:0914”(association)0.350
GALCHSPA5psi-mi:“MI:0914”(association)0.350
CABP2PPM1Apsi-mi:“MI:0914”(association)0.350
OTUD6BGALCpsi-mi:“MI:0914”(association)0.350
ESS2CDC40psi-mi:“MI:0914”(association)0.350

BioGRID (53): GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS), GALC (Affinity Capture-MS)

ESM2 similar proteins: A1D0A3, A1D1Z9, A1D8Y6, A1DJ58, A2QEQ6, B0XMP7, B0XXE7, B0Y224, B5X3C1, B8N6V7, B8QGZ3, D4B5H9, H2DF88, O02791, P29000, P29853, P45582, P48980, P48981, P54803, P54804, P54818, P80065, P93761, Q0C8J3, Q0CUG5, Q0VA39, Q10NX8, Q2UCU3, Q39041, Q43348, Q43857, Q498K0, Q4R1C4, Q4WE86, Q4WG05, Q4WS33, Q5AVP1, Q5AZ53, Q5B7X2

Diamond homologs: B5X3C1, O02791, P54803, P54804, P54818, Q0VA39, Q498K0, Q5SNX7, Q95QT2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1639 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic192
Likely pathogenic147
Uncertain significance425
Likely benign561
Benign114

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1066093NM_000153.4(GALC):c.1987del (p.Trp663fs)Pathogenic
1070140NC_000014.8:g.(?_88391504)_88423173delPathogenic
1070141NC_000014.8:g.(?_88391504)_88423174delPathogenic
1070539NM_000153.4(GALC):c.181_182insAG (p.Val61fs)Pathogenic
1070766NM_000153.4(GALC):c.302_308dup (p.Gly104fs)Pathogenic
1070767NM_000153.4(GALC):c.176del (p.Gly59fs)Pathogenic
1071897NM_000153.4(GALC):c.1884del (p.Lys628fs)Pathogenic
1071955NM_000153.4(GALC):c.1762_1763del (p.Leu588fs)Pathogenic
1072645NM_000153.4(GALC):c.37C>T (p.Arg13Ter)Pathogenic
1073890NM_000153.4(GALC):c.498del (p.Asn167fs)Pathogenic
1073951NC_000014.8:g.(?_88391503)_88423172delPathogenic
1074198NM_000153.4(GALC):c.1411_1432del (p.Thr471fs)Pathogenic
1074616NM_000153.4(GALC):c.332del (p.Gly111fs)Pathogenic
1298354NM_000153.4(GALC):c.1964del (p.Pro655fs)Pathogenic
1299228NM_000153.4(GALC):c.1821dup (p.Thr608fs)Pathogenic
1299585NM_000153.4(GALC):c.396G>A (p.Trp132Ter)Pathogenic
1320177NM_000153.4(GALC):c.688_694del (p.Trp230fs)Pathogenic
1322975NM_000153.4(GALC):c.1531del (p.Thr511fs)Pathogenic
1322976NM_000153.4(GALC):c.1736_1739del (p.Ala579fs)Pathogenic
1331457NM_000153.4(GALC):c.683_694delinsCTC (p.Asn228_Ser232delinsThrPro)Pathogenic
1364954NM_000153.4(GALC):c.1815dup (p.Arg606fs)Pathogenic
1378825NM_000153.4(GALC):c.1648dup (p.Ser550fs)Pathogenic
1385679NM_000153.4(GALC):c.782_783dup (p.Asp262fs)Pathogenic
1402125NM_000153.4(GALC):c.505C>T (p.Gln169Ter)Pathogenic
1413114NM_000153.4(GALC):c.1291G>T (p.Gly431Ter)Pathogenic
1414629NM_000153.4(GALC):c.27del (p.Trp10fs)Pathogenic
1424701NM_000153.4(GALC):c.29G>A (p.Trp10Ter)Pathogenic
1425129NM_000153.4(GALC):c.1270C>T (p.Gln424Ter)Pathogenic
1432015NM_000153.4(GALC):c.1367_1368del (p.Leu456fs)Pathogenic
1451476NM_000153.4(GALC):c.283_284del (p.Leu95fs)Pathogenic

SpliceAI

2455 predictions. Top by Δscore:

VariantEffectΔscore
14:87934745:T:TAdonor_gain1.0000
14:87945668:T:Cacceptor_gain1.0000
14:87945668:T:TCacceptor_gain1.0000
14:87947723:CTCA:Cdonor_loss1.0000
14:87947726:A:ACdonor_gain1.0000
14:87947726:AC:Adonor_gain1.0000
14:87947727:C:CAdonor_gain1.0000
14:87947727:CC:Cdonor_gain1.0000
14:87947727:CCA:Cdonor_gain1.0000
14:87947727:CCAA:Cdonor_gain1.0000
14:87947874:AGGAG:Aacceptor_gain1.0000
14:87947875:GGAG:Gacceptor_gain1.0000
14:87947876:GAG:Gacceptor_gain1.0000
14:87947876:GAGCT:Gacceptor_gain1.0000
14:87947877:AG:Aacceptor_gain1.0000
14:87947877:AGC:Aacceptor_gain1.0000
14:87947878:GC:Gacceptor_gain1.0000
14:87947879:C:CAacceptor_loss1.0000
14:87947879:C:CCacceptor_gain1.0000
14:87947879:CT:Cacceptor_gain1.0000
14:87949928:CACT:Cacceptor_gain1.0000
14:87949930:CTCTG:Cacceptor_loss1.0000
14:87949931:TC:Tacceptor_loss1.0000
14:87949932:C:CCacceptor_gain1.0000
14:87949933:T:Aacceptor_loss1.0000
14:87950657:A:ACdonor_gain1.0000
14:87950658:C:CCdonor_gain1.0000
14:87950747:CT:Cacceptor_gain1.0000
14:87963508:TGAG:Tacceptor_gain1.0000
14:87963512:C:CCacceptor_gain1.0000

AlphaMissense

4492 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:87965619:A:GW307R0.997
14:87965619:A:TW307R0.997
14:87945573:A:CS550R0.996
14:87945573:A:TS550R0.996
14:87945575:T:GS550R0.996
14:87945631:C:GR531P0.996
14:87992979:G:CS62R0.996
14:87992979:G:TS62R0.996
14:87992981:T:GS62R0.996
14:87965602:A:CS312R0.995
14:87965602:A:TS312R0.995
14:87965604:T:GS312R0.995
14:87984444:A:GW178R0.995
14:87984444:A:TW178R0.995
14:87968374:C:GR290P0.994
14:87934797:C:GA665P0.993
14:87982233:T:AE198V0.993
14:87982235:A:CN197K0.993
14:87982235:A:TN197K0.993
14:87984525:A:GW151R0.993
14:87984525:A:TW151R0.993
14:87941494:C:GA579P0.992
14:87945634:A:GL530P0.991
14:87963427:A:GL373P0.991
14:87968432:A:GW271R0.991
14:87968432:A:TW271R0.991
14:87984510:A:GW156R0.991
14:87984510:A:TW156R0.991
14:87986540:A:GW131R0.991
14:87986540:A:TW131R0.991

dbSNP variants (sampled 300 via entrez): RS1000118702 (14:87972797 G>A), RS1000206216 (14:87954044 C>G,T), RS1000236059 (14:87970221 T>A,C), RS1000267264 (14:87969969 G>A), RS1000294367 (14:87949557 A>G), RS1000380667 (14:87960269 G>A), RS1000404443 (14:87957062 C>T), RS1000410233 (14:87986401 G>A), RS1000577837 (14:87982885 C>T), RS1000597596 (14:87977152 A>G), RS1000671098 (14:87948860 A>C), RS1000687893 (14:87988863 A>G), RS1000734560 (14:87955699 T>C), RS1000753136 (14:87960415 T>C), RS1000755207 (14:87942735 G>A)

Disease associations

OMIM: gene MIM:606890 | disease phenotypes: MIM:245200, MIM:108600, MIM:312080, MIM:301500

GenCC curated gene-disease

DiseaseClassificationInheritance
Krabbe diseaseDefinitiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
Krabbe diseaseDefinitiveAR

Mondo (12): Krabbe disease (MONDO:0009499), spastic ataxia (MONDO:0017845), congenital nervous system disorder (MONDO:0002320), epilepsy syndrome (MONDO:0015650), intellectual disability (MONDO:0001071), movement disorder (MONDO:0005395), amblyopia (MONDO:0001020), strabismus (MONDO:0003432), pathologic nystagmus (MONDO:0004843), fetal growth restriction (MONDO:0005030), leukodystrophy (MONDO:0019046), Fabry disease (MONDO:0010526)

Orphanet (6): Krabbe disease (Orphanet:487), Spastic ataxia (Orphanet:316226), Epilepsy syndrome (Orphanet:166463), Leukodystrophy (Orphanet:68356), Fabry disease (Orphanet:324), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

133 total (30 of 133 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000020Urinary incontinence
HP:0000238Hydrocephalus
HP:0000365Hearing impairment
HP:0000467Neck muscle weakness
HP:0000505Visual impairment
HP:0000565Esotropia
HP:0000572Visual loss
HP:0000613Photophobia
HP:0000618Blindness
HP:0000639Nystagmus
HP:0000648Optic atrophy
HP:0000649Abnormality of visual evoked potentials
HP:0000708Atypical behavior
HP:0000712Emotional lability
HP:0000726Dementia
HP:0000737Irritability
HP:0000762Decreased nerve conduction velocity
HP:0001053Hypopigmented skin patches
HP:0001188Hand clenching
HP:0001250Seizure
HP:0001251Ataxia
HP:0001252Hypotonia
HP:0001257Spasticity
HP:0001260Dysarthria
HP:0001263Global developmental delay
HP:0001264Spastic diplegia
HP:0001265Hyporeflexia
HP:0001268Mental deterioration
HP:0001270Motor delay

GWAS associations

25 associations (top):

StudyTraitp-value
GCST000879_38Crohn’s disease4.000000e-18
GCST001648_1Breast cancer4.000000e-06
GCST001725_48Inflammatory bowel disease2.000000e-14
GCST001995_7Adverse response to chemotherapy (neutropenia/leucopenia) (docetaxel)2.000000e-06
GCST002797_2Pulmonary artery enlargement in chronic obstructive pulmonary disease4.000000e-08
GCST002929_17Chromium levels2.000000e-06
GCST003181_6Staphylococcus aureus nasal carriage (intermittent)9.000000e-07
GCST003487_14Response to fenofibrate (total cholesterol levels)3.000000e-06
GCST004131_90Inflammatory bowel disease3.000000e-11
GCST004132_113Crohn’s disease5.000000e-12
GCST004735_28Epstein-Barr virus copy number in lymphoblastoid cell lines1.000000e-06
GCST004902_53Parkinson’s disease9.000000e-11
GCST005531_60Multiple sclerosis2.000000e-20
GCST005752_63Systemic lupus erythematosus5.000000e-10
GCST005944_3Viral capsid antigen IgG seropositivity7.000000e-10
GCST009325_18Parkinson’s disease or first degree relation to individual with Parkinson’s disease6.000000e-11
GCST009391_1491Metabolite levels4.000000e-07
GCST009391_1895Metabolite levels3.000000e-06
GCST009391_1954Metabolite levels8.000000e-06
GCST009391_224Metabolite levels3.000000e-06
GCST009597_29Multiple sclerosis3.000000e-07
GCST010988_542Adult body size6.000000e-09
GCST012006_6Intralaminar thalamic nuclei volume1.000000e-09
GCST90002379_65Basophil count6.000000e-15
GCST90002380_28Basophil percentage of white cells8.000000e-17

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0006347pulmonary artery enlargement
EFO:0007758intermittent Staphylococcus aureus carrier status
EFO:0007806total cholesterol change measurement
EFO:0009272Epstein Barr viral capsid antigen seropositivity
EFO:0010416triacylglycerol 52:4 measurement
EFO:0010414triacylglycerol 52:2 measurement
EFO:0010423triacylglycerol 54:5 measurement
EFO:0010491glycocholate measurement
EFO:0006935thalamus volume
EFO:0005090basophil count
EFO:0007992basophil percentage of leukocytes

MeSH disease descriptors (9)

DescriptorNameTree numbers
D000550AmblyopiaC10.228.140.055; C10.597.751.941.073; C11.966.073; C23.888.592.763.941.073
D000795Fabry DiseaseC10.228.140.163.100.435.825.200; C10.228.140.300.275.374; C14.907.253.329.374; C16.320.322.124; C16.320.565.189.435.825.200; C16.320.565.398.641.803.300; C16.320.565.595.554.825.200; C18.452.132.100.435.825.200; C18.452.584.563.641.803.300; C18.452.648.189.435.825.200; C18.452.648.398.641.803.300; C18.452.648.595.554.825.200
D005317Fetal Growth RetardationC12.050.703.277.370; C16.300.390; C23.550.393.450
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D007965Leukodystrophy, Globoid CellC10.228.140.163.100.362.500; C10.228.140.163.100.435.825.590; C10.228.140.695.625.500; C10.314.400.500; C16.320.565.189.362.500; C16.320.565.189.435.825.590; C16.320.565.398.641.803.585; C16.320.565.595.554.825.590; C18.452.132.100.362.500; C18.452.132.100.435.825.590; C18.452.584.563.641.803.585; C18.452.648.189.362.500; C18.452.648.189.435.825.590; C18.452.648.398.641.803.585; C18.452.648.595.554.825.590
D009069Movement DisordersC10.228.662
D009759Nystagmus, PathologicC10.292.562.675; C11.590.400
D013285StrabismusC10.292.562.887; C11.590.810
C564815Spastic Ataxia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3713095 (SINGLE PROTEIN)

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

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.50Kd3179nMCHEMBL3752910
5.50ED503179nMCHEMBL3752910
5.06Kd8725nMCHEMBL5653589
5.06ED508725nMCHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 7 total; 2 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-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148411: Binding affinity to human GALC incubated for 45 mins by Kinobead based pull down assaykd3.1788uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148411: Binding affinity to human GALC incubated for 45 mins by Kinobead based pull down assaykd8.7254uM

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression7
sodium arseniteaffects methylation, decreases expression4
(+)-JQ1 compoundaffects expression, decreases expression3
entinostatdecreases expression, affects cotreatment2
methylmercuric chloridedecreases expression1
bisphenol Aincreases methylation1
arseniteaffects binding, increases reaction1
butyraldehydedecreases expression1
potassium chromate(VI)decreases expression1
nickel sulfatedecreases expression1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphindecreases expression, affects cotreatment1
bisphenol Sdecreases methylation1
Arbutinincreases expression1
Benzo(a)pyreneincreases methylation1
Cannabidioldecreases expression1
Cyclophosphamideaffects response to substance1
Estradioldecreases expression1
Fenfluramineincreases expression1
Rotenoneincreases expression1
Tretinoinincreases expression1
Acrylamidedecreases expression1

ChEMBL screening assays

3 unique, capped per target: 2 binding, 1 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3562110FunctionalPubChem BioAssay. A Novel Cell-Based Assay to Identify Small Molecules for B -Galactocerebrosidase. (Class of assay: confirmatory)PubChem BioAssay data set
CHEMBL4258350BindingInhibition of recombinant human GALC at pH 5.2 pre-incubated for 10 mins followed by 4-methylumbelliferyl-beta-D-galactopyranoside substrate addition and measured after 20 mins by fluorescence assayOrthoester functionalized N-guanidino derivatives of 1,5-dideoxy-1,5-imino-d-xylitol as pH-responsive inhibitors of β-glucocerebrosidase. — Medchemcomm

Cellosaurus cell lines

13 cell lines: 5 finite cell line, 4 induced pluripotent stem cell, 3 transformed cell line, 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_2Z50GM04372Finite cell lineMale
CVCL_2Z51GM04517Finite cell lineMale
CVCL_2Z54GM06805Transformed cell lineFemale
CVCL_2Z55GM06806Finite cell lineFemale
CVCL_2Z56GM06807Transformed cell lineMale
CVCL_2Z57GM06808Finite cell lineFemale
CVCL_2Z58GM06809Transformed cell lineFemale
CVCL_2Z59GM06810Finite cell lineMale
CVCL_A9YVPUMCi001-AInduced pluripotent stem cellMale
CVCL_A9YWPUMCi002-AInduced pluripotent stem cellMale

Clinical trials (associated diseases)

223 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
NCT04639310PHASE3TERMINATEDXEN496 (Ezogabine) in Children With KCNQ2 Developmental and Epileptic Encephalopathy
NCT04912856PHASE3TERMINATEDAn Open-Label Extension of the Study XEN496 (Ezogabine) in Children With KCNQ2-DEE
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
NCT00383448PHASE2COMPLETEDHSCT for High Risk Inherited Inborn Errors
NCT00668564PHASE2TERMINATEDHematopoietic Stem Cell Transplantation (HCT) for Inborn Errors of Metabolism
NCT01043640PHASE2COMPLETEDAllogeneic Bone Marrow Transplant for Inherited Metabolic Disorders
NCT02171104PHASE2ACTIVE_NOT_RECRUITINGMT2013-31: Allo HCT for Metabolic Disorders and Severe Osteopetrosis
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)
NCT00176904PHASE2/PHASE3COMPLETEDStem Cell Transplant for Inborn Errors of Metabolism
NCT01372228PHASE1/PHASE2TERMINATEDPhase I/II Pilot Study of Mixed Chimerism to Treat Inherited Metabolic Disorders
NCT04693598PHASE1/PHASE2ACTIVE_NOT_RECRUITINGGene Transfer Clinical Trial for Krabbe Disease
NCT05739643PHASE1/PHASE2ACTIVE_NOT_RECRUITINGGene Transfer Clinical Trial for Infantile and Late Infantile Krabbe Disease Treated Previously With HSCT
NCT00005900Not specifiedUNKNOWNStudy of Pulmonary Complications in Pediatric Patients With Storage Disorders Undergoing Allogeneic Hematopoietic Stem Cell Transplantation
NCT00787865Not specifiedACTIVE_NOT_RECRUITINGDiffusion Tensor Imaging (DTI) in Infants With Krabbe Disease
NCT01425489Not specifiedWITHDRAWNBiomarker for Krabbe Disease (BioKrabbe)
NCT01938014Not specifiedCOMPLETEDLysosomal Storage Disease: Health, Development, and Functional Outcome Surveillance in Preschool Children
NCT02699190Not specifiedCOMPLETEDLeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies
NCT02993796Not specifiedRECRUITINGKrabbe Disease Global Patient Registry
NCT03047369Not specifiedRECRUITINGThe Myelin Disorders Biorepository Project
NCT03333200Not specifiedRECRUITINGLongitudinal Study of Neurodegenerative Disorders
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns
NCT06308718Not specifiedTERMINATEDLong-term Follow-up Study to Evaluate Safety and Efficacy of FBX-101 in Krabbe Patients
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT04297891Not specifiedUNKNOWNPhenotypes, Biomarkers and Pathophysiology in Spastic Ataxias
NCT04048213Not specifiedUNKNOWNThe Becoming of Children With Doose Syndrome
NCT05097742Not specifiedCOMPLETEDCognitive Impairments in Children With Epilepsy
NCT06222840Not specifiedCOMPLETEDElectro-clinical Features and Functional Connectivity Analysis in SYN1 Gene Mutation-related Epilepsy
NCT06223334Not specifiedUNKNOWNEpileptic Syndromes in Infants and Early Childhood