HK1

protein-coding

hexokinase 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

NM_000188.3

Inheritance

AR, AD

ClinVar variants

P:41U:446B:225

Top phenotype

Anemia, congenital, nonspherocytic hemolytic, 5

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr10:69,269,984-69,401,884

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~131.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

non-spherocytic hemolytic anemia due to hexokinase deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009340

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosa 79STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0044320

Submitter: Labcorp Genetics (formerly Invitae)

neurodevelopmental disorder with visual defects and brain anomaliesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032807

Submitter: Labcorp Genetics (formerly Invitae)

Charcot-Marie-Tooth disease type 4GSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011534

Submitter: PanelApp Australia

non-spherocytic hemolytic anemia due to hexokinase deficiencyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0009340

Submitter: Ambry Genetics

neurodevelopmental disorder with visual defects and brain anomaliesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032807

Submitter: PanelApp Australia

neurodevelopmental disorder with visual defects and brain anomaliesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032807

Submitter: G2P

hyperinsulinismSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0002177

Submitter: PanelApp Australia

retinitis pigmentosa 79STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0044320

Submitter: PanelApp Australia

Charcot-Marie-Tooth disease type 4GSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011534

Submitter: Orphanet

retinitis pigmentosa 79LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0044320

Submitter: G2P

non-spherocytic hemolytic anemia due to hexokinase deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009340

Submitter: Orphanet

neurodevelopmental disorder with visual defects and brain anomaliesMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0032807

Submitter: Ambry Genetics

non-spherocytic hemolytic anemia due to hexokinase deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009340

Submitter: PanelApp Australia

Charcot-Marie-Tooth disease type 4GLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0011534

Submitter: Ambry Genetics

retinitis pigmentosa 79MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0044320

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Anemia, congenital, nonspherocytic hemolytic, 5AR

Manifestation: Hematologic; Musculoskeletal; Neurologic; Ophthalmologic

Intervention: Hematologic

Rationale: Individuals may manifest with severe hemolysis, and anemia may be sufficiently severe to require splenectomy

Refs: 6015552; 27532; 7234862; 6848140; 7655856; 12393545; 19536174; 19608687; 22978647; 25190649; 25316723; 30778173Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HK1 variants in ClinVar

16 Conditions Cataloged
not providedTotal: 765
not specifiedTotal: 157
HK1-related disorderTotal: 91
Inborn genetic diseasesTotal: 75
Retinal dystrophyTotal: 39
Neurodevelopmental disorder with visual defects and brain anomaliesTotal: 39
Hemolytic anemia due to hexokinase deficiencyTotal: 20
Retinitis pigmentosa 79Total: 16

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
212
clinvar
4
clinvar
221
missense
2
clinvar
19
clinvar
426
clinvar
7
clinvar
2
clinvar
456
nonsense
4
clinvar
3
clinvar
1
clinvar
8
start loss
0
frameshift
4
clinvar
6
clinvar
6
clinvar
16
splice donor/acceptor (+/-2bp)
3
clinvar
8
clinvar
11
Total10314462196712

Highest pathogenic variant AF is 0.000014249692

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000188.3RefSeqNP_000179.218MANE Select
ENST00000359426.7EnsemblENSP00000352398.618MANE Select
NM_001322364.2RefSeqNP_001309293.119Standard
NM_001322365.2RefSeqNP_001309294.120Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.233415550.6140.00003716078
Missense (PolyPhen)93224.040.415112446
Synonymous0.7312102240.9380.00001611814
Loss of Function4.96843.20.1850.00000256499

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000180.00018rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000220.00022rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000970.000097rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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