HYI

hydroxypyruvate isomerase (putative)

Basic information

Region (hg38): 1:43450988-43453989

Links

ENSG00000178922 ∙ NCBI:81888 ∙ OMIM:619128 ∙ HGNC:26948 ∙ Uniprot:Q5T013 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (12 variants)
• not provided (5 variants)
• not specified (2 variants)
• Developmental and epileptic encephalopathy, 18 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HYI 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				1		1
missense			12	2	2	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding			2			2
Total	0	0	14	3	2

Variants in HYI

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

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

Position	Type	Phenotype	Significance	ClinVar
1-43451250-C-T			Likely benign (May 18, 2018)
1-43451261-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-43451268-A-C			Likely benign (Aug 31, 2017)
1-43451281-C-T		not specified	Uncertain significance (Mar 27, 2023)
1-43451427-C-G			Benign (May 18, 2018)
1-43451539-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-43451672-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-43451813-G-A			Likely benign (Feb 01, 2024)
1-43451930-C-T			Likely benign (Aug 08, 2017)
1-43452196-CT-C		Developmental and epileptic encephalopathy, 18	Uncertain significance (Sep 03, 2021)
1-43452224-G-C		not specified	Uncertain significance (Jun 23, 2021)
1-43452257-A-G		not specified	Uncertain significance (Dec 19, 2022)
1-43452278-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-43452338-G-C		not specified	Uncertain significance (Oct 25, 2023)
1-43453102-C-T		Developmental and epileptic encephalopathy, 18	Uncertain significance (Dec 31, 2021)
1-43453395-C-T			Likely benign (Aug 24, 2017)
1-43453434-T-C		not specified	Uncertain significance (Dec 17, 2021)
1-43453438-G-C		not specified	Uncertain significance (Oct 05, 2021)
1-43453447-C-T		not specified	Uncertain significance (Jul 26, 2022)
1-43453627-C-T		not specified	Benign (May 04, 2022)
1-43453676-G-C		not specified	Uncertain significance (Jan 05, 2022)
1-43453697-C-G		not specified	Uncertain significance (Jul 06, 2021)
1-43453702-C-T		not specified	Uncertain significance (May 11, 2022)
1-43453771-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HYI	protein_coding	protein_coding	ENST00000372425	8	2837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-14	0.00458	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.905	167	137	1.22	0.00000748	1688
Missense in Polyphen		65	54.596	1.1906		695
Synonymous	-1.40	67	53.9	1.24	0.00000283	550
Loss of Function	-0.774	19	15.7	1.21	9.12e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000384	0.000383
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00131	0.00131
Finnish	0.00	0.00
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.00131	0.00131
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the reversible isomerization between hydroxypyruvate and 2-hydroxy-3-oxopropanoate (also termed tartronate semialdehyde). {ECO:0000250}.
• Pathway: Glyoxylate and dicarboxylate metabolism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.934
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.3

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.197
• ghis: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.520

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hyi

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;protein binding;hydroxypyruvate isomerase activity;racemase and epimerase activity, acting on carbohydrates and derivatives