GALK1 (galactokinase 1)

Gene

• Entrez ID: 2584
• Gene name: Galactokinase 1
• Gene symbol: GALK1
• Synonyms (NCBI Gene): GALK, GK1, HEL-S-19
• Chromosome: 17
• Chromosome location: 17q25.1
• Summary: Galactokinase is a major enzyme for the metabolism of galactose and its deficiency causes congenital cataracts during infancy and presenile cataracts in the adult population. [provided by RefSeq, Jul 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs80084721	G>A,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs104894572	G>A,T	Pathogenic	Missense variant, coding sequence variant
rs104894577	C>A	Pathogenic	Stop gained, coding sequence variant
rs113464656	C>A,G,T	Likely-pathogenic	Splice donor variant
rs376790302	G>A	Pathogenic	Coding sequence variant, missense variant
rs759284637	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs767329054	C>-,CC	Pathogenic-likely-pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs770087254	GCCTGGGCCGTGCGCCGAATCT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs771067891	->GC	Likely-pathogenic	Frameshift variant, coding sequence variant
rs915070690	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant
rs1311294794	T>C,G	Likely-pathogenic	Missense variant, initiator codon variant
rs1555748534	->GGTACTCGCTGGAGGCCAGGGAG	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555748556	C>T	Likely-pathogenic	Splice acceptor variant
rs1555748940	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1568395061	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1599335144	C>-	Pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT029752	hsa-miR-26b-5p	Microarray	19088304
MIRT040306	hsa-miR-615-3p	CLASH	23622248
MIRT036546	hsa-miR-1225-5p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004335	Function	Galactokinase activity	EXP	7542884
GO:0004335	Function	Galactokinase activity	IBA
GO:0004335	Function	Galactokinase activity	IDA	7542884, 12694189
GO:0004335	Function	Galactokinase activity	IEA
GO:0004335	Function	Galactokinase activity	TAS
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005524	Function	ATP binding	IDA	12694189
GO:0005524	Function	ATP binding	IEA
GO:0005534	Function	Galactose binding	IDA	14596685
GO:0005534	Function	Galactose binding	IEA
GO:0005737	Component	Cytoplasm	IDA	8908517
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006012	Process	Galactose metabolic process	IBA
GO:0006012	Process	Galactose metabolic process	IEA
GO:0006012	Process	Galactose metabolic process	IEA
GO:0006012	Process	Galactose metabolic process	IMP	15024738
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IDA	8908517
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016773	Function	Phosphotransferase activity, alcohol group as acceptor	IEA
GO:0019402	Process	Galactitol metabolic process	IEA
GO:0033499	Process	Galactose catabolic process via UDP-galactose, Leloir pathway	IEA
GO:0033499	Process	Galactose catabolic process via UDP-galactose, Leloir pathway	TAS
GO:0046835	Process	Carbohydrate phosphorylation	IEA
GO:0061623	Process	Glycolytic process from galactose	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867

Other IDs

• MIM: 604313
• HGNC: 4118
• e!Ensembl: ENSG00000108479

Protein

• UniProt ID: P51570
• Protein name: Galactokinase (EC 2.7.1.6) (Galactose kinase)
• Protein function: Catalyzes the transfer of a phosphate from ATP to alpha-D-galactose and participates in the first committed step in the catabolism of galactose.
• PDB: 1WUU, 6GR2, 6Q3W, 6Q3X, 6Q8Z, 6Q90, 6Q91, 6QJE, 6ZFH, 6ZGV, 6ZGW, 6ZGX, 6ZGY, 6ZGZ, 6ZH0, 7OZX, 7RCL, 7RCM, 7S49, 7S4C
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF10509	GalKase_gal_bdg	18 → 67	Galactokinase galactose-binding signature	Domain
  PF00288	GHMP_kinases_N	126 → 194	GHMP kinases N terminal domain	Family
  PF08544	GHMP_kinases_C	291 → 374	GHMP kinases C terminal	Family

• Sequence:

  MAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELM
  TVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAA
  PLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGM
  PCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRR
  RQCEEVARALGKESLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDY
  RAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASA
  APHAMRHIQEHYGGTATFYLSQAADGAKVLCL

• Sequence length: 392

Pathways

KEGG:

Galactose metabolism
Amino sugar and nucleotide sugar metabolism
Metabolic pathways
Biosynthesis of nucleotide sugars

Reactome:

Defective GALK1 can cause Galactosemia II (GALCT2)
Galactose catabolism

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Deficiency of galactokinase	Likely pathogenic; Pathogenic	rs2545899470, rs775843885, rs2143608501, rs2143603585, rs767790909, rs2143601360, rs142772020, rs2061564118, rs2143608720, rs2143608028, rs2143605190, rs767799179, rs2143586633, rs2061596711, rs2143585254, rs2143605351, rs2545904183, rs1363497653, rs2545903733, rs2545903771, rs2545903117, rs2061599170, rs2545900373, rs2545903471, rs773991014, rs1599336146, rs980603321, rs759699355, rs1474376359, rs104894577, rs104894572, rs111033608, rs1599335144, rs2545903700, rs2545900296, rs770871380, rs2545903185, rs2061598689, rs2545903484, rs2545903458, rs2545900232, rs1224987754, rs2545900350, rs2545900132, rs2545900206, rs1555748556, rs1311294794, rs2545899596, rs769550271, rs2545899880, rs2545905243, rs2545900183, rs200095299, rs2545903065, rs2545904210, rs1362123883, rs2545899422, rs1422073677, rs756290185, rs2504221771, rs2545903420, rs2545900278, rs1555747776, rs113464656, rs754967473, rs1026685248, rs770087254, rs771067891, rs1555748940, rs371517491, rs753571180, rs1555748534, rs767329054, rs1555748926, rs1247635972, rs375690568, rs1568395061, rs376790302, rs2061599016, rs982043960, rs773559496, rs2061594762, rs2061563475, rs2061592335, rs1599335132, rs575077063, rs2061598873, rs761638957	RCV004576134 RCV001381964 RCV001390010 RCV001580707 RCV001995252 RCV001950940 RCV001980343 RCV001867375 RCV001993333 RCV001899504 RCV002037728 RCV001959046 RCV002010483 RCV001958764 RCV001886221 RCV002244285 RCV002309740 RCV002310051 RCV002307925 RCV002308079 RCV002309154 RCV002306959 RCV002307023 RCV002307274 RCV002310531 RCV002308387 RCV003087871 RCV002572257 RCV002650389 RCV000005983 RCV000005984 RCV000005985 RCV000005986 RCV002912944 RCV002909178 RCV003032220 RCV003025167 RCV003155602 RCV003461622 RCV003461623 RCV003461625 RCV003461626 RCV003461627 RCV003461628 RCV003505482 RCV003505847 RCV003506160 RCV003506269 RCV003506347 RCV003506588 RCV003504976 RCV003505616 RCV003613572 RCV003613901 RCV003613713 RCV003613803 RCV003614565 RCV003614698 RCV003614817 RCV003615155 RCV003879325 RCV004576133 RCV004576640 RCV004576641 RCV000666379 RCV000670419 RCV000669015 RCV000673382 RCV000674786 RCV000670947 RCV000666168 RCV000671410 RCV000672148 RCV000666699 RCV000673596 RCV000674206 RCV000667929 RCV000671906 RCV000674134 RCV000669565 RCV000674666 RCV001232085 RCV001844235 RCV000800933 RCV001070440 RCV001215181 RCV001229403 RCV001225611 RCV001246394 RCV001263817 RCV001263818 RCV001263819 RCV001263820 RCV001263986	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
GALK1-related disorder	Likely pathogenic; Pathogenic	rs759699355, rs375690568	RCV004754883 RCV004754550	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CATARACT	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPIDERMOLYSIS BULLOSA, JUNCTIONAL 5A, INTERMEDIATE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPIDERMOLYSIS BULLOSA, JUNCTIONAL 5B, WITH PYLORIC ATRESIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALACTOSEMIA II	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALACTOSEMIAS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUNCTIONAL EPIDERMOLYSIS BULLOSA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WEBER-COCKAYNE SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adult junctional epidermolysis bullosa (disorder)	Junctional Epidermolysis Bullosa	CLINVAR_DG	10484780, 12485428		★☆☆☆☆ Found in Text Mining only
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	33115496	Associate	★☆☆☆☆ Found in Text Mining only
Blindness	Blindness	Pubtator	10521295	Associate	★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	32807972, 38353984	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	BEFREE	10570908, 11231902, 11978883, 12705493, 15003454, 15024738, 2122118, 29580649, 29893426, 3951827, 7670469		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cataract	Cataract	Pubtator	12694189, 12942049, 173185, 32807972, 8908517	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cataract	Cataract	CTD_human_DG	7670469		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cataract	Cataract	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Classical galactosemia	Galactosemia	BEFREE	12350230, 12694189, 15003454, 22632133, 27789348, 28672748, 28961353, 29893426, 3043741, 30806949, 31808946, 9540406		★☆☆☆☆ Found in Text Mining only
Classical galactosemia	Galactosemia	CTD_human_DG	7670469		★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	32807972	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	2004848		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	35963622	Associate	★☆☆☆☆ Found in Text Mining only
Congenital cataract	Congenital Cataract	BEFREE	20405025, 22632133, 24211322, 7670469		★☆☆☆☆ Found in Text Mining only
Deficiency of galactokinase	Deficiency Of Galactokinase	BEFREE	10521295, 10790206, 11139256, 11231902, 11978884, 15024738, 15526155, 15590630, 29893426, 3949470, 7670469		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Deficiency of galactokinase	Deficiency Of Galactokinase	GENOMICS_ENGLAND_DG	10521295, 27604308		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Deficiency of galactokinase	Deficiency Of Galactokinase	ORPHANET_DG	10521295		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Deficiency of galactokinase	Deficiency Of Galactokinase	CLINVAR_DG	10521295, 10570908, 10790206, 11978883, 11978884, 12647253, 12694189, 20405025, 21290184		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Deficiency of galactokinase	Deficiency Of Galactokinase	UNIPROT_DG	10521295, 10790206, 11139256, 11231902, 12694189, 15024738		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Deficiency of galactokinase	Deficiency Of Galactokinase	CTD_human_DG	7670469		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Epidermolysis bullosa with pyloric atresia	Epidermolysis Bullosa	CLINVAR_DG	10484780, 12485428		★☆☆☆☆ Found in Text Mining only
Galactokinase deficiency	Galactokinase Deficiency	Orphanet			★☆☆☆☆ Found in Text Mining only
Galactosemias	Galactosemia	Pubtator	10521295, 12694189, 173185, 18490662, 29261178, 32807972, 34088690, 8908517	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galactosemias	Galactosemia	BEFREE	12350230, 12694189, 15003454, 16988899, 22632133, 28672748, 28961353, 29893426, 3043741, 30806949, 31808946, 9540406		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galactosemias	Galactosemia	LHGDN	15526155, 15590630		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galactosemias	Galactosemia	Pubtator	20863731	Inhibit	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galactosemias	Galactosemia	CTD_human_DG	7670469		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hemorrhagic Disorders	Hemorrhagic disease	Pubtator	32807972	Associate	★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	9540406		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	27919945		★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	BEFREE	27919945		★☆☆☆☆ Found in Text Mining only
Melanocytic nevus	Melanocytic nevus	BEFREE	22632133		★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic Diseases	BEFREE	28672748		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	2004848		★☆☆☆☆ Found in Text Mining only
Nevus	Nevus	BEFREE	22632133		★☆☆☆☆ Found in Text Mining only
Presenile cataract	Presenile Cataract	BEFREE	3951827, 7352874, 74495, 7670469		★☆☆☆☆ Found in Text Mining only
Pseudoaphakia	Cataract	CTD_human_DG	7670469		★☆☆☆☆ Found in Text Mining only
UDPglucose 4-epimerase deficiency disease	UDPglucose 4-Epimerase Deficiency Disease	BEFREE	11279193, 28672748		★☆☆☆☆ Found in Text Mining only
UDPglucose 4-epimerase deficiency disease	UDPglucose 4-Epimerase Deficiency Disease	CTD_human_DG	7670469		★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	33545950, 37834386	Associate	★☆☆☆☆ Found in Text Mining only
Weber-Cockayne Syndrome	Epidermolysis bullosa simplex	CLINVAR_DG	10484780, 12485428		★★☆☆☆ Found in Text Mining + Unknown/Other Associations