HKDC1 (hexokinase domain containing 1)

Gene

• Entrez ID: 80201
• Gene name: Hexokinase domain containing 1
• Gene symbol: HKDC1
• Synonyms (NCBI Gene): RP92
• Chromosome: 10
• Chromosome location: 10q22.1
• Summary: This gene encodes a member of the hexokinase protein family. The encoded protein is involved in glucose metabolism, and reduced expression may be associated with gestational diabetes mellitus. High expression of this gene may also be associated with poor

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs148723879	C>T	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs200034765	C>A,T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs201518882	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs759709025	C>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022488	hsa-miR-124-3p	Microarray	18668037
MIRT1048220	hsa-miR-1264	CLIP-seq
MIRT1048221	hsa-miR-1266	CLIP-seq
MIRT1048222	hsa-miR-1287	CLIP-seq
MIRT1048223	hsa-miR-2117	CLIP-seq
MIRT1048224	hsa-miR-2277-3p	CLIP-seq
MIRT1048225	hsa-miR-3123	CLIP-seq
MIRT1048226	hsa-miR-3130-3p	CLIP-seq
MIRT1048227	hsa-miR-3183	CLIP-seq
MIRT1048228	hsa-miR-320a	CLIP-seq
MIRT1048229	hsa-miR-320b	CLIP-seq
MIRT1048230	hsa-miR-320c	CLIP-seq
MIRT1048231	hsa-miR-320d	CLIP-seq
MIRT1048232	hsa-miR-3620	CLIP-seq
MIRT1048233	hsa-miR-3622a-3p	CLIP-seq
MIRT1048234	hsa-miR-3622b-3p	CLIP-seq
MIRT1048235	hsa-miR-3652	CLIP-seq
MIRT1048236	hsa-miR-3664-3p	CLIP-seq
MIRT1048237	hsa-miR-375	CLIP-seq
MIRT1048238	hsa-miR-3925-5p	CLIP-seq
MIRT1048239	hsa-miR-3973	CLIP-seq
MIRT1048240	hsa-miR-3976	CLIP-seq
MIRT1048241	hsa-miR-4273	CLIP-seq
MIRT1048242	hsa-miR-4283	CLIP-seq
MIRT1048243	hsa-miR-4292	CLIP-seq
MIRT1048244	hsa-miR-4429	CLIP-seq
MIRT1048245	hsa-miR-4430	CLIP-seq
MIRT1048246	hsa-miR-4436a	CLIP-seq
MIRT1048247	hsa-miR-4489	CLIP-seq
MIRT1048248	hsa-miR-4492	CLIP-seq
MIRT1048249	hsa-miR-4498	CLIP-seq
MIRT1048250	hsa-miR-4499	CLIP-seq
MIRT1048251	hsa-miR-4518	CLIP-seq
MIRT1048252	hsa-miR-4677-5p	CLIP-seq
MIRT1048253	hsa-miR-4723-3p	CLIP-seq
MIRT1048254	hsa-miR-4753-3p	CLIP-seq
MIRT1048255	hsa-miR-4766-5p	CLIP-seq
MIRT1048256	hsa-miR-4793-3p	CLIP-seq
MIRT1048257	hsa-miR-520g	CLIP-seq
MIRT1048258	hsa-miR-520h	CLIP-seq
MIRT1048259	hsa-miR-762	CLIP-seq
MIRT2010966	hsa-miR-628-5p	CLIP-seq
MIRT1048221	hsa-miR-1266	CLIP-seq
MIRT2243179	hsa-miR-1294	CLIP-seq
MIRT2243180	hsa-miR-3157-5p	CLIP-seq
MIRT2243181	hsa-miR-3646	CLIP-seq
MIRT1048236	hsa-miR-3664-3p	CLIP-seq
MIRT1048246	hsa-miR-4436a	CLIP-seq
MIRT2243182	hsa-miR-4459	CLIP-seq
MIRT1048251	hsa-miR-4518	CLIP-seq
MIRT2243183	hsa-miR-4691-3p	CLIP-seq
MIRT2243184	hsa-miR-4710	CLIP-seq
MIRT2243185	hsa-miR-4772-3p	CLIP-seq
MIRT2243186	hsa-miR-4779	CLIP-seq
MIRT2243187	hsa-miR-665	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0001678	Process	Intracellular glucose homeostasis	IBA
GO:0001678	Process	Intracellular glucose homeostasis	IDA	30517626
GO:0001678	Process	Intracellular glucose homeostasis	IEA
GO:0001917	Component	Photoreceptor inner segment	IEA
GO:0004340	Function	Glucokinase activity	IBA
GO:0004340	Function	Glucokinase activity	IDA	30517626
GO:0004340	Function	Glucokinase activity	IEA
GO:0004396	Function	Hexokinase activity	IEA
GO:0005524	Function	ATP binding	IEA
GO:0005536	Function	D-glucose binding	IEA
GO:0005737	Component	Cytoplasm	IDA	30085091
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	30517626
GO:0005739	Component	Mitochondrion	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005975	Process	Carbohydrate metabolic process	IEA
GO:0006006	Process	Glucose metabolic process	IBA
GO:0006096	Process	Glycolytic process	IBA
GO:0006096	Process	Glycolytic process	IEA
GO:0008865	Function	Fructokinase activity	IBA
GO:0016020	Component	Membrane	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016773	Function	Phosphotransferase activity, alcohol group as acceptor	IEA
GO:0019318	Process	Hexose metabolic process	IEA
GO:0019637	Process	Organophosphate metabolic process	IEA
GO:0031966	Component	Mitochondrial membrane	IEA
GO:0046835	Process	Carbohydrate phosphorylation	IEA
GO:0051156	Process	Glucose 6-phosphate metabolic process	IBA
GO:0051156	Process	Glucose 6-phosphate metabolic process	IDA	30517626
GO:1901135	Process	Carbohydrate derivative metabolic process	IEA

Other IDs

• MIM: 617221
• HGNC: 23302
• e!Ensembl: ENSG00000156510

Protein

• UniProt ID: Q2TB90
• Protein name: Hexokinase HKDC1 (EC 2.7.1.1) (Hexokinase domain-containing protein 1)
• Protein function: Catalyzes the phosphorylation of hexose to hexose 6-phosphate, although at very low level compared to other hexokinases (PubMed:30517626). Has low glucose phosphorylating activity compared to other hexokinases (PubMed:30517626). Involved in gluc
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00349	Hexokinase_1	21 → 219	Hexokinase	Domain
  PF03727	Hexokinase_2	225 → 459	Hexokinase	Domain
  PF00349	Hexokinase_1	469 → 666	Hexokinase	Domain
  PF03727	Hexokinase_2	672 → 906	Hexokinase	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed (PubMed:27459389, PubMed:29401404). Highly expressed in the brush border, surface epithelium and the myenteric plexus of the small and large intestines; the acinar centrocytes and interlobular ducts of the pancreas; an
• Sequence:

  MFAVHLMAFYFSKLKEDQIKKVDRFLYHMRLSDDTLLDIMRRFRAEMEKGLAKDTNPTAA
  VKMLPTFVRAIPDGSENGEFLSLDLGGSKFRVLKVQVAEEGKRHVQMESQFYPTPNEIIR
  GNGTELFEYVADCLADFMKTKDLKHKKLPLGLTFSFPCRQTKLEEGVLLSWTKKFKARGV
  QDTDVVSRLTKAMRRHKDMDVDILALVNDTVGTMMTCAYDDPYCEVGVIIGTGTNACYME
  DMSNIDLVEGDEGRMCINTEWGAFGDDGALEDIRTEFDRELDLGSLNPGKQLFEKMISGL
  YLGELVRLILLKMAKAGLLFGGEKSSALHTKGKIETRHVAAMEKYKEGLANTREILVDLG
  LEPSEADCIAVQHVCTIVSFRSANLCAAALAAILTRLRENKKVERLRTTVGMDGTLYKIH
  PQYPKRLHKVVRKLVPSCDVRFLLSESGSTKGAAMVTAVASRVQAQRKQIDRVLALFQLT
  REQLVDVQAKMRAELEYGLKKKSHGLATVRMLPTYVCGLPDGTEKGKFLALDLGGTNFRV
  LLVKIRSGRRSVRMYNKIFAIPLEIMQGTGEELFDHIVQCIADFLDYMGLKGASLPLGFT
  FSFPCRQMSIDKGTLIGWTKGFKATDCEGEDVVDMLREAIKRRNEFDLDIVAVVNDTVGT
  MMTCGYEDPNCEIGLIAGTGSNMCYMEDMRNIEMVEGGEGKMCINTEWGGFGDNGCIDDI
  WTRYDTEVDEGSLNPGKQRYEKMTSGMYLGEIVRQILIDLTKQGLLFRGQISERLRTRGI
  FETKFLSQIESDRLALLQVRRILQQLGLDSTCEDSIVVKEVCGAVSRRAAQLCGAGLAAI
  VEKRREDQGLEHLRITVGVDGTLYKLHPHFSRILQETVKELAPRCDVTFMLSEDGSGKGA
  ALITAVAKRLQQAQKEN

• Sequence length: 917

Pathways

KEGG:

Glycolysis / Gluconeogenesis
Fructose and mannose metabolism
Galactose metabolism
Starch and sucrose metabolism
Amino sugar and nucleotide sugar metabolism
Neomycin, kanamycin and gentamicin biosynthesis
Metabolic pathways
Carbon metabolism
Biosynthesis of nucleotide sugars
HIF-1 signaling pathway
Insulin signaling pathway
Type II diabetes mellitus
Carbohydrate digestion and absorption
Shigellosis
Central carbon metabolism in cancer

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
Nonsyndromic cleft lip palate	Likely pathogenic	rs759709025	RCV000755128	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa 92	Likely pathogenic	rs142379141, rs2539918923, rs2539897956	RCV001779345 RCV003990493 RCV003990655	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short stature	Likely pathogenic	rs1564726619, rs148723879	RCV000736152 RCV000736153	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CIRRHOSIS OF LIVER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GESTATIONAL DIABETES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Keratoconus 1	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
LIVER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Long QT syndrome	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	20732627	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	31058090		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	36519789	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	24162464		★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	33991070, 34044809	Associate	★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	Pubtator	34971568	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	30005951		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	32503434	Associate	★☆☆☆☆ Found in Text Mining only
Deafness	Deafness	Pubtator	35248088	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Gestational	Gestational diabetes	Pubtator	25648650	Inhibit	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	35485648	Stimulate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	34763315	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	35485648	Associate	★☆☆☆☆ Found in Text Mining only
GATA2 Deficiency	Gata2 deficiency	Pubtator	33423158	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	35248088	Associate	★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	25648650		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	BEFREE	27703147		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	Pubtator	27703147	Associate	★☆☆☆☆ Found in Text Mining only
LATE-ONSET RETINAL DEGENERATION (disorder)	RETINAL DEGENERATION	BEFREE	30085091		★☆☆☆☆ Found in Text Mining only
Liver Neoplasms	Liver neoplasm	Pubtator	34763315	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	31058090		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	24162464		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24162464		★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	33423158	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	35689754	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30005951, 31058090		★☆☆☆☆ Found in Text Mining only
Non-alcoholic Fatty Liver Disease	Non-Alcoholic Fatty Liver Disease	BEFREE	30517626		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	30085091		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Stomach Neoplasms	Stomach neoplasms	Pubtator	36519789	Stimulate	★☆☆☆☆ Found in Text Mining only