HK1
protein-codinghexokinase 1
Gene summary
Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. This gene encodes a ubiquitous form of hexokinase which localizes to the outer membrane of mitochondria. Mutations in this gene have been associated with hemolytic anemia due to hexokinase deficiency. Alternative splicing of this gene results in several transcript variants which encode different isoforms, some of which are tissue-specific. [provided by RefSeq, Apr 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~131.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009340
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0044320
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0032807
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0011534
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009340
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0032807
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0032807
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0002177
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0044320
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0011534
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0044320
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009340
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0032807
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0009340
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0011534
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0044320
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Hematologic; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: Hematologic
Rationale: Individuals may manifest with severe hemolysis, and anemia may be sufficiently severe to require splenectomy
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HK1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000188.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | 212 | 4 | 221 | ||
| missense | 2 | 19 | 426 | 7 | 2 | 456 |
| nonsense | 4 | 3 | 1 | 8 | ||
| start loss | 0 | |||||
| frameshift | 4 | 6 | 6 | 16 | ||
| splice donor/acceptor (+/-2bp) | 3 | 8 | 11 | |||
| Total | 10 | 31 | 446 | 219 | 6 | 712 |
Highest pathogenic variant AF is 0.000014249692
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000179.2 | 18 | MANE Select | |
| Ensembl | ENSP00000352398.6 | 18 | MANE Select | |
| RefSeq | NP_001309293.1 | 19 | Standard | |
| RefSeq | NP_001309294.1 | 20 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- cellular glucose homeostasis
- positive regulation of cytokine secretion involved in immune response
- glycolytic process
- carbohydrate phosphorylation
- positive regulation of interleukin-1 beta secretion
Molecular Function
- glucokinase activity
- hexokinase activity
- protein binding
- ATP binding
- glucose binding
Cellular Component
- mitochondrion
- mitochondrial outer membrane
- cytosol
- membrane raft
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000404387
- Coding exons
- 19
- Length
- 131899
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 23
- Defined
- 125748
- p
- 0.0000915
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.23 | 341 | 555 | 0.614 | 0.0000371 | 6078 |
| Missense (PolyPhen) | 93 | 224.04 | 0.41511 | 2446 | ||
| Synonymous | 0.731 | 210 | 224 | 0.938 | 0.0000161 | 1814 |
| Loss of Function | 4.96 | 8 | 43.2 | 0.185 | 0.00000256 | 499 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Disease
- DISEASE: Hexokinase deficiency (HK deficiency) [MIM:235700]: Rare autosomal recessive disease with nonspherocytic hemolytic anemia as the predominant clinical feature. {ECO:0000269|PubMed:12393545, ECO:0000269|PubMed:7655856}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Neuropathy, hereditary motor and sensory, Russe type (HMSNR) [MIM:605285]: An autosomal recessive progressive complex peripheral neuropathy characterized by onset in the first decade of distal lower limb weakness and muscle atrophy resulting in walking difficulties. Distal impairment of the upper limbs usually occurs later, as does proximal lower limb weakness. There is distal sensory impairment, with pes cavus and areflexia. Laboratory studies suggest that it is a myelinopathy resulting in reduced nerve conduction velocities in the demyelinating range as well as a length-dependent axonopathy. {ECO:0000269|PubMed:19536174}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 79 (RP79) [MIM:617460]: A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP79 inheritance is autosomal dominant. {ECO:0000269|PubMed:25190649, ECO:0000269|PubMed:25316723}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.802
Intolerance Scores
- LoFtool
- 0.0552
- RVIS EVS
- -1.22
- RVIS percentile EVS
- 5.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |