HYKK

hydroxylysine kinase

Basic information

Region (hg38): 15:78507563-78537372

Previous symbols: [ "AGPHD1" ]

Links

ENSG00000188266 ∙ NCBI:123688 ∙ OMIM:614681 ∙ HGNC:34403 ∙ Uniprot:A2RU49 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inborn disorder of lysine and hydroxylysine metabolism (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

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

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HYKK 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						0
missense			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in HYKK

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

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

Position	Type	Phenotype	Significance	ClinVar
15-78513114-C-T		not specified	Uncertain significance (Jan 03, 2024)
15-78513242-G-A		not specified	Likely benign (Mar 06, 2023)
15-78513261-G-A		not specified	Uncertain significance (Mar 24, 2023)
15-78513378-C-T		not specified	Uncertain significance (Jan 23, 2023)
15-78515007-T-C		not specified	Uncertain significance (Feb 23, 2023)
15-78515018-C-T		not specified	Uncertain significance (Mar 01, 2024)
15-78515039-C-A		not specified	Likely benign (Nov 15, 2021)
15-78515061-T-C		not specified	Uncertain significance (May 26, 2023)
15-78515075-A-G		not specified	Uncertain significance (Feb 22, 2023)
15-78527424-C-G		not specified	Uncertain significance (Nov 08, 2022)
15-78527443-G-A		not specified	Uncertain significance (May 24, 2023)
15-78527507-A-G		not specified	Uncertain significance (Mar 04, 2024)
15-78527522-T-A		not specified	Uncertain significance (Nov 10, 2022)
15-78533266-G-A		not specified	Uncertain significance (Mar 24, 2023)
15-78533267-C-T		not specified	Uncertain significance (Jul 10, 2023)
15-78533312-G-T		not specified	Uncertain significance (May 22, 2023)
15-78533322-C-G		not specified	Uncertain significance (Feb 27, 2023)
15-78533374-G-A		not specified	Uncertain significance (Dec 13, 2023)
15-78533417-G-A		not specified	Uncertain significance (Nov 09, 2023)
15-78533551-A-C		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HYKK	protein_coding	protein_coding	ENST00000388988	4	29809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000733	0.746	122609	11	2182	124802	0.00882

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.673	171	198	0.865	0.00000963	2457
Missense in Polyphen		52	62.615	0.83047		791
Synonymous	-0.0597	74	73.3	1.01	0.00000375	709
Loss of Function	1.16	10	14.8	0.675	8.39e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00983	0.00968
Ashkenazi Jewish	0.00526	0.00508
East Asian	0.000242	0.000222
Finnish	0.0108	0.0108
European (Non-Finnish)	0.0139	0.0135
Middle Eastern	0.000242	0.000222
South Asian	0.00352	0.00340
Other	0.00951	0.00861

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the GTP-dependent phosphorylation of 5- hydroxy-L-lysine. {ECO:0000269|PubMed:22241472}.
• Pathway: Lysine degradation - Homo sapiens (human);Lysine catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Metabolism (Consensus)

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.216
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hykk

Gene ontology

• Biological process: lysine catabolic process;phosphorylation
• Cellular component: mitochondrial matrix
• Molecular function: protein binding;hydroxylysine kinase activity