HKDC1

hexokinase domain containing 1

Basic information

Region (hg38): 10:69220332-69267552

Links

ENSG00000156510 ∙ NCBI:80201 ∙ OMIM:617221 ∙ HGNC:23302 ∙ Uniprot:Q2TB90 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 92	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	30085091

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HKDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HKDC1 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		2	76	4	2	84
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	76	6	4

Variants in HKDC1

This is a list of pathogenic ClinVar variants found in the HKDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-69227231-C-T		not specified	Uncertain significance (Mar 31, 2024)
10-69227267-C-T		not specified	Uncertain significance (Oct 05, 2022)
10-69227269-G-T			Likely benign (Nov 01, 2022)
10-69227273-C-T		not specified	Uncertain significance (Sep 06, 2022)
10-69227277-C-T		not specified	Uncertain significance (May 30, 2024)
10-69227316-C-T		Retinitis pigmentosa 92	Pathogenic (Nov 11, 2021)
10-69227340-C-T			Benign (Jan 19, 2018)
10-69227345-G-A		not specified	Uncertain significance (Apr 08, 2022)
10-69232787-G-A		Retinitis pigmentosa 92	Likely pathogenic (Mar 29, 2024)
10-69232818-A-C		not specified	Uncertain significance (Apr 13, 2022)
10-69232838-G-C		not specified	Uncertain significance (Dec 21, 2022)
10-69232838-G-T		Short stature	Likely pathogenic (Nov 18, 2001)
10-69232861-G-C		not specified	Uncertain significance (Dec 21, 2022)
10-69232863-G-A		not specified	Uncertain significance (Dec 02, 2022)
10-69232865-C-G		not specified	Uncertain significance (Sep 15, 2021)
10-69232895-C-T		not specified	Uncertain significance (Sep 14, 2022)
10-69232896-G-A		not specified	Uncertain significance (Oct 03, 2022)
10-69232898-G-A		Retinitis pigmentosa 92	Uncertain significance (Apr 04, 2024)
10-69239079-G-A		not specified	Uncertain significance (Mar 26, 2024)
10-69239130-G-C		not specified	Uncertain significance (Aug 02, 2021)
10-69240664-G-A		not specified	Uncertain significance (Sep 26, 2023)
10-69240720-C-A		not specified	Uncertain significance (Jan 09, 2024)
10-69240740-G-T		not specified	Uncertain significance (Nov 16, 2021)
10-69243220-A-G		not specified	Uncertain significance (May 27, 2022)
10-69243253-A-T		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HKDC1	protein_coding	protein_coding	ENST00000354624	18	47257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-14	0.925	125586	1	160	125747	0.000640

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.137	583	574	1.02	0.0000351	6016
Missense in Polyphen		205	222.61	0.9209		2355
Synonymous	0.276	231	236	0.977	0.0000159	1830
Loss of Function	2.18	29	44.7	0.648	0.00000273	478

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00203	0.00201
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00103	0.00103
Finnish	0.000519	0.000508
European (Non-Finnish)	0.000676	0.000642
Middle Eastern	0.00103	0.00103
South Asian	0.000492	0.000457
Other	0.000361	0.000326

dbNSFP

Source: dbNSFP

• Pathway: UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II;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);trehalose degradation (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 70.88

Haploinsufficiency Scores

• pHI: 0.586
• hipred: Y
• hipred_score: 0.589
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.151

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hkdc1
• Phenotype: homeostasis/metabolism 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); liver/biliary system phenotype

Gene ontology

• Biological process: cellular glucose homeostasis;glycolytic process;hexose metabolic process;carbohydrate phosphorylation;glucose 6-phosphate metabolic process
• Cellular component: mitochondrion;cytosol
• Molecular function: glucokinase activity;ATP binding;glucose binding;fructokinase activity;mannokinase activity