HYI

protein-coding

hydroxypyruvate isomerase (putative)

Gene summary

This gene encodes a putative hydroxypyruvate isomerase, which likely catalyzes the conversion of hydroxypyruvate to 2-hydroxy-3-oxopropanoate, and may be involved in carbohydrate transport and metabolism. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

MANE transcript

NM_001190880.3

Inheritance

—

ClinVar variants

U:50B:11

Top phenotype

Developmental and epileptic encephalopathy, 18

gnomAD constraint

pLI —, LoF o/e 1.21

Max pathogenic AF

—

Genomic locus

chr1:43,450,989-43,453,989

External References & Databases

Ensembl (ENSG00000178922)

Transcript & Mutation Effects

hg38 • Region Span ~3.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HYI variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 11

Developmental and epileptic encephalopathy, 18Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001190880.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	7 clinvar		9
missense			48 clinvar	2 clinvar	2 clinvar	52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	9	2	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001190880.3	RefSeq	NP_001177809.1	8	MANE Select
ENST00000372430.9	Ensembl	ENSP00000361507.4	8	MANE Select
NM_001243526.2	RefSeq	NP_001230455.1	9	Standard
NM_001330526.2	RefSeq	NP_001317455.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glyoxylate and dicarboxylate metabolism - Homo sapiens (human)

Biological Process

biological_process

Molecular Function

molecular_function
protein binding
hydroxypyruvate isomerase activity
racemase and epimerase activity, acting on carbohydrates and derivatives

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372425
Coding exons: 8
Length: 2837
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 125748
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.905	167	137	1.22	0.00000748	1688
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0013	0.0013	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the reversible isomerization between hydroxypyruvate and 2-hydroxy-3-oxopropanoate (also termed tartronate semialdehyde). {ECO:0000250}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.934
RVIS EVS: 0.84
RVIS percentile EVS: 88.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.520

Gene Damage Prediction

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