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

retinitis pigmentosa (Limited), mode of inheritance: AR

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.

not_specified (156 variants)
Retinitis_pigmentosa_92 (9 variants)
not_provided (8 variants)
Short_stature (3 variants)
Nonsyndromic_cleft_lip_palate (2 variants)
Long_QT_syndrome (1 variants)
Keratoconus_1 (1 variants)

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. These statistics are base on transcript: NM_000025130.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	2 clinvar	4
missense		5 clinvar	156 clinvar	7 clinvar	1 clinvar	169
nonsense		1 clinvar		1 clinvar		2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	6	157	10	3

Highest pathogenic variant AF is 0.000143117

Loading clinvar variants...

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

loftool
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