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Intellectual disability

Gene: HK1

Green List (high evidence)

HK1 (hexokinase 1)
EnsemblGeneIds (GRCh38): ENSG00000156515
EnsemblGeneIds (GRCh37): ENSG00000156515
OMIM: 142600, Gene2Phenotype
HK1 is in 7 panels

5 reviews

Ivone Leong (Genomics England Curator)

Comment on list classification: Promoted from red to green. This gene is associated with a phenotype in OMIM but not in Gene2Phenotype. There are sufficient cases for this gene to be promote to green status. Variants on the 5' end of the gene have been associated with neuropathy, hereditary motor and sensory, Russe type.
Created: 9 Jul 2019, 4:13 p.m. | Last Modified: 9 Jul 2019, 4:13 p.m.
Panel Version: 2.949
Comment on mode of pathogenicity: A gain of function effect is presumed to cause disease.
Created: 9 Jul 2019, 4:08 p.m. | Last Modified: 9 Jul 2019, 4:08 p.m.
Panel Version: 2.948

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Okur et al. (2019 - PMID: 30778173) report on 7 individuals from 6 unrelated families, all harboring de novo HK1 variants. The common phenotype consisted among others of DD (7/7), ID (5/5 - the other 2 individuals were too young to evaluate), visual impairment (7/7 - optic atrophy and/or retinitis pigmentosa) and brain MRI abnormalities (6/7). Other features included tone abnormalities, delayed/impaired speech, ataxia, feeding problems, etc.

All variants were missense and occurred as de novo events. The following 4 variants were reported (using NM_000188.2 as reference):
- c.1241G>A p.(Gly414Glu)
- c.1252A>G p.(Lys418Glu)
- c.1334C>T p.(Ser445Leu) [observed in 2 unrelated individuals]
- c.1370C>T p.(Thr457Met) [observed in 2 sibs as well as well as a 3rd affected unrelated subject, the parents of the sibs and a further unaffected child from the same family were not found to harbor the variant]

As commented on, NM_000188.2:c.1334C>T p.(Ser445Leu) [or NM_033497.2:c.1346C>T (p.Ser449Leu)] and NM_000188.2:c.1370C>T p.(Thr457Met) [or NM_033497.2:c.1382C>T (p.Thr461Met)] were recurrent variants in this study and previously reported in 2 additional subjects from the DDD study (where 4 de novo variants were observed in total - PMID: 28135719). [All relevant DDD subjects are summarized in the denovo-db : http://denovo-db.gs.washington.edu/denovo-db/QueryVariantServlet?searchBy=Gene&target=HK1].

HK1 encodes hexokinase 1. Hexokinases catalyze the first step in glucose metabolism (glycolytic pathway), using ATP as phosphate donor for the phosphorylation of glucose to glucose-6-phosphate (G6P). The 4 hexokinases (the 3 other - HK2, HK3 and HK4 - being encoded by other genes) vary in tissue distribution and other properties. HK1 has the predominant glucose phosphorylating activity in tissues with strict dependence on glucose utilization for their physiologic functions, such as brain, erythrocytes, etc (better summarized by Bianchi et al. - PMID: 9197463). Different HK1 isoforms exist, with the canonical one expressed ubiquitously and known as "brain-type hexokinase" due to its abundance in brain (summarized by Okur et al).

All aforementioned variants affect all HK1 isoforms. In silico predictions were (mostly) suggestive of pathogenicity. The variants were absent from ExAC/gnomAD databases (where HK1 has a pLI of 0.91 and Z-score of 3.34).

Hexokinase activity in RBCs from 2 affected subjects was found to be normal (as has also been the case for HK1-related phenotypes other than non-spherocytic anemia - details below). A gain-of-function effect is presumed. No additional studies have been carried out.

Based on this study and OMIM, previously reported HK1-related phenotypes include:
- Bi-allelic HK1 variants affecting hexokinase activity cause Hemolytic anemia (HA) due to hexokinase deficiency (MIM 235700). On 5 occasions neurodevelopmental phenotypes have been reported in individuals with this diagnosis although - as suggested - not all cases were molecularly confirmed and/or these findings might have been secondary to intrauterine consequences of HA or coincidental (PMIDs cited by Okur et al - table 3 : 5076409, 655151, 4052330, 12211198, 27282571).
- Homozygous 5' UTR variants have been associated with Neuropathy, hereditary motor and sensory, Russe type (MIM 605285).
- A missense variant (c.2539G>A or p.Glu847Lys) close to the C-terminal end has been reported in several occurences of (AD) retinitis pigmentosa 79 (MIM 617460) segregating with the disorder. Asymptomatic heterozygous carriers have also been reported. One patient homozygous for this variant presented with early-onset visual impairment but without hemolytic anemia or developmental anomalies.
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HK1 is not associated with any phenotype in G2P.
The gene is included in gene panels for ID offered by some diagnostic laboratories (eg. GeneDx - among the authors of the study).
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As a result this gene can be considered for upgrade to green (DD/ID in 7 individuals or possibly more when considering the DDD study participants) or amber (no functional evidence).
Created: 24 Feb 2019, 9:46 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Abnormal muscle tone, Global developmental delay, Intellectual disability, Visual impairment, Neurological speech impairment, Ataxia

Publications

Variants in this GENE are reported as part of current diagnostic practice

Eleanor Williams (Genomics England Curator)

Comment on list classification: Associated with Hemolytic anemia due to hexokinase deficiency (MIM:235700), Neuropathy, hereditary motor and sensory, Russe type (MIM:605285) and Retinitis pigmentosa 79 (MIM:617460) in OMIM. No evidence found of association with Intellectual Disability in OMIM, Gene2Phenotype or PubMed searches.
Created: 21 Feb 2018, 10:59 a.m.

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_movement_disorder_list . Main mutation mechanism : NA
Created: 27 Jul 2017, 6:34 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : manju_list; neuro_20160418_strict; NA. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 12:37 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

  • Personal communication with NIHRBRRD BRIDGE SPEED

Louise Daugherty (Genomics England Curator)

Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 11:59 a.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Hemolytic anemia due to hexokinase deficiency, 235700
  • Neuropathy, hereditary motor and sensory, Russe type, 605285
  • Abnormal muscle tone
  • Global developmental delay
  • Intellectual disability
  • Visual impairment
  • Neurological speech impairment
  • Ataxia
Tags
missense
OMIM
142600
Clinvar variants
Variants in HK1
Penetrance
Complete
Publications
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Panels with this gene

History Filter Activity

9 Jul 2019, Gel status: 3

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: hk1 has been classified as Green List (High Evidence).

9 Jul 2019, Gel status: 1

Set mode of pathogenicity

Ivone Leong (Genomics England Curator)

Mode of pathogenicity for gene: HK1 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

9 Jul 2019, Gel status: 1

Set Phenotypes

Ivone Leong (Genomics England Curator)

Phenotypes for gene: HK1 were changed from Hemolytic anemia due to hexokinase deficiency, 235700; Neuropathy, hereditary motor and sensory, Russe type, 605285 to Hemolytic anemia due to hexokinase deficiency, 235700; Neuropathy, hereditary motor and sensory, Russe type, 605285; Abnormal muscle tone; Global developmental delay; Intellectual disability; Visual impairment; Neurological speech impairment; Ataxia

9 Jul 2019, Gel status: 1

Set publications

Ivone Leong (Genomics England Curator)

Publications for gene: HK1 were set to

9 Jul 2019, Gel status: 1

Added Tag

Ivone Leong (Genomics England Curator)

Tag missense tag was added to gene: HK1.

12 Mar 2018, Gel status: 1

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

12 Mar 2018, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

Expert Review Red was added to HK1. Panel: Intellectual disability

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

HK1 was created by BRIDGE

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

HK1 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene