HK3

hexokinase 3

Basic information

Region (hg38): 5:176880869-176899346

Links

ENSG00000160883 ∙ NCBI:3101 ∙ OMIM:142570 ∙ HGNC:4925 ∙ Uniprot:P52790 ∙ 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 HK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HK3 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				2	2	4
missense			78	7	2	87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding						0
Total	0	0	78	9	4

Variants in HK3

This is a list of pathogenic ClinVar variants found in the HK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-176881080-C-T		not specified	Uncertain significance (Feb 15, 2023)
5-176881111-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-176881135-C-T		not specified	Uncertain significance (Jun 30, 2023)
5-176881147-C-T		not specified	Uncertain significance (Dec 03, 2024)
5-176881155-A-C		not specified	Uncertain significance (Aug 28, 2024)
5-176881217-G-A		not specified	Likely benign (Jul 30, 2024)
5-176881303-G-A		not specified	Uncertain significance (Jul 10, 2024)
5-176881307-G-C		not specified	Uncertain significance (Oct 13, 2023)
5-176881333-C-T		not specified	Uncertain significance (Aug 26, 2022)
5-176881336-C-G		not specified	Uncertain significance (Aug 11, 2024)
5-176881374-C-T		not specified	Uncertain significance (Jan 05, 2022)
5-176881375-G-A		not specified	Uncertain significance (Jun 21, 2023)
5-176881387-C-T		not specified	Uncertain significance (Apr 22, 2024)
5-176881411-A-G		not specified	Uncertain significance (Oct 13, 2023)
5-176881497-T-C		not specified	Uncertain significance (Feb 17, 2022)
5-176881530-C-T		not specified	Uncertain significance (Mar 26, 2024)
5-176881735-T-C		not specified	Uncertain significance (Jan 30, 2024)
5-176881736-C-A		not specified	Uncertain significance (Sep 17, 2021)
5-176881743-C-T		not specified	Uncertain significance (Aug 01, 2024)
5-176881762-G-A		not specified	Uncertain significance (Sep 13, 2023)
5-176881771-C-T		not specified	Uncertain significance (Apr 20, 2024)
5-176881822-A-T		not specified	Uncertain significance (Feb 28, 2023)
5-176881954-C-T		not specified	Uncertain significance (Jun 22, 2023)
5-176881983-G-C			Benign (Oct 09, 2017)
5-176881992-C-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HK3	protein_coding	protein_coding	ENST00000292432	18	18464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.60e-23	0.00523	125551	1	196	125748	0.000784

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0277	593	595	0.997	0.0000389	5897
Missense in Polyphen		269	271.82	0.98964		2795
Synonymous	-0.680	267	253	1.05	0.0000169	1995
Loss of Function	0.681	37	41.7	0.886	0.00000214	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00172	0.00171
Ashkenazi Jewish	0.00	0.00
East Asian	0.00169	0.00169
Finnish	0.000107	0.0000924
European (Non-Finnish)	0.000813	0.000809
Middle Eastern	0.00169	0.00169
South Asian	0.000948	0.000915
Other	0.000817	0.000815

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);Pathways in clear cell renal cell carcinoma;PI3K-AKT-mTOR - VitD3 Signalling;Glycolysis and Gluconeogenesis;Neutrophil degranulation;Aminosugars metabolism;Metabolism of carbohydrates;Fructose Mannose metabolism;Glycolysis Gluconeogenesis;Innate Immune System;Immune System;Metabolism;Glycolysis;GDP-glucose biosynthesis II;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Glucose metabolism;Galactose metabolism (Consensus)

Recessive Scores

• pRec: 0.188

Intolerance Scores

• loftool: 0.0604
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.55

Haploinsufficiency Scores

• pHI: 0.813
• hipred: N
• hipred_score: 0.280
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.713

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hk3

Gene ontology

• Biological process: cellular glucose homeostasis;glycolytic process;neutrophil degranulation;carbohydrate phosphorylation;glucose 6-phosphate metabolic process;canonical glycolysis
• Cellular component: extracellular region;cytosol;secretory granule lumen;ficolin-1-rich granule lumen
• Molecular function: glucokinase activity;hexokinase activity;ATP binding;glucose binding;fructokinase activity;mannokinase activity