HK2

hexokinase 2

Basic information

Region (hg38): 2:74834127-74893359

Links

ENSG00000159399 ∙ NCBI:3099 ∙ OMIM:601125 ∙ HGNC:4923 ∙ Uniprot:P52789 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HK2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				14	6	20
missense			55	3	4	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	55	17	11

Variants in HK2

This is a list of pathogenic ClinVar variants found in the HK2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-74834625-C-G		not specified	Uncertain significance (Mar 17, 2023)
2-74854341-G-A		not specified	Uncertain significance (Apr 25, 2023)
2-74854353-C-T		not specified	Uncertain significance (Jan 10, 2022)
2-74854359-C-T		not specified	Uncertain significance (Jun 23, 2023)
2-74854425-A-G		not specified	Uncertain significance (Aug 17, 2021)
2-74867690-G-T		not specified	Uncertain significance (May 29, 2024)
2-74867737-C-A		not specified	Uncertain significance (Aug 17, 2022)
2-74867748-C-T		HK2-related disorder	Likely benign (Apr 09, 2019)
2-74867791-C-A			Likely benign (Jun 27, 2018)
2-74872350-A-T		HK2-related disorder	Benign (Oct 28, 2019)
2-74872389-G-A		HK2-related disorder	Likely benign (Aug 20, 2019)
2-74873281-C-T		HK2-related disorder	Likely benign (Apr 25, 2019)
2-74873334-T-C		not specified	Uncertain significance (Aug 22, 2022)
2-74873342-C-G		not specified	Uncertain significance (Jan 23, 2024)
2-74873346-T-A		not specified	Uncertain significance (Jul 19, 2023)
2-74873348-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-74873381-G-A		HK2-related disorder	Benign (Apr 25, 2019)
2-74873855-C-T		HK2-related disorder	Likely benign (Feb 27, 2019)
2-74873929-T-C		not specified	Uncertain significance (Aug 23, 2021)
2-74874327-T-C		HK2-related disorder	Benign (Oct 23, 2019)
2-74874328-G-A		not specified	Uncertain significance (Apr 11, 2023)
2-74874357-G-C		not specified	Uncertain significance (May 04, 2023)
2-74874364-T-C		not specified	Uncertain significance (Aug 30, 2022)
2-74874436-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-74874437-C-T		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HK2	protein_coding	protein_coding	ENST00000290573	18	59379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00459	0.995	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	477	553	0.862	0.0000382	6040
Missense in Polyphen		151	221.87	0.68059		2578
Synonymous	-1.32	243	218	1.11	0.0000155	1801
Loss of Function	4.11	12	40.1	0.299	0.00000234	469

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000427	0.000423
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Fructose and mannose metabolism - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Type II diabetes mellitus - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Starch and sucrose metabolism - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Galactose metabolism - Homo sapiens (human);Neomycin, kanamycin and gentamicin biosynthesis - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Glycogen synthetase deficiency;Glycogenosis, Type III. Cori disease, Debrancher glycogenosis;Mucopolysaccharidosis VI. Sly syndrome;Sucrase-isomaltase deficiency;Glycogenosis, Type IV. Amylopectinosis, Anderson disease;Glycogenosis, Type VI. Hers disease;Warburg Effect;Glycolysis;Glycogenosis, Type VII. Tarui disease;Gluconeogenesis;Starch and Sucrose Metabolism;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Fanconi-bickel syndrome;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Glycogenosis, Type IB;Pathways in clear cell renal cell carcinoma;Glycolysis and Gluconeogenesis;Aminosugars metabolism;Metabolism of carbohydrates;Fructose Mannose metabolism;Glycolysis Gluconeogenesis;Metabolism;Glycolysis;GDP-glucose biosynthesis II;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Glucose metabolism;HIF-1-alpha transcription factor network;Galactose metabolism (Consensus)

Recessive Scores

• pRec: 0.458

Intolerance Scores

• loftool: 0.0828
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.38

Haploinsufficiency Scores

• pHI: 0.544
• hipred: Y
• hipred_score: 0.637
• ghis: 0.439

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hk2
• Phenotype: cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; neoplasm

Gene ontology

• Biological process: response to hypoxia;cellular glucose homeostasis;response to ischemia;glycolytic process;lactation;apoptotic mitochondrial changes;negative regulation of mitochondrial membrane permeability;positive regulation of angiogenesis;regulation of glucose import;carbohydrate phosphorylation;glucose 6-phosphate metabolic process;canonical glycolysis;establishment of protein localization to mitochondrion;maintenance of protein location in mitochondrion;positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization;cellular response to leukemia inhibitory factor;negative regulation of reactive oxygen species metabolic process
• Cellular component: mitochondrial outer membrane;cytosol;plasma membrane;membrane;sarcoplasmic reticulum
• Molecular function: glucokinase activity;hexokinase activity;protein binding;ATP binding;glucose binding;fructokinase activity;mannokinase activity