HAGHL

protein-coding

hydroxyacylglutathione hydrolase like, the group of MBL domain containing glyoxalase 2 subfamily

Gene summary

Predicted to enable hydroxyacylglutathione hydrolase activity. Predicted to be involved in obsolete methylglyoxal catabolic process to pyruvate via (R)-S-lactoyl-glutathione. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032304.4

Inheritance

—

ClinVar variants

U:67B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr16:726,936-735,525

External References & Databases

Ensembl (ENSG00000103253)

Transcript & Mutation Effects

hg38 • Region Span ~8.6 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 HAGHL variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 67

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032304.4. 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						0
missense			65 clinvar	3 clinvar		68
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	67	3	0	70

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 73 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032304.4	RefSeq	NP_115680.1	8	MANE Select
ENST00000389703.8	Ensembl	ENSP00000374353.3	8	MANE Select
NM_001290137.2	RefSeq	NP_001277066.1	8	Standard
NM_001290139.2	RefSeq	NP_001277068.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pyruvate metabolism

Molecular Function

hydrolase activity
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389703
Coding exons: 8
Length: 8590
Individuals with no LoFs: 124748
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124763
p: 0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.724	166	142	1.17	0.00000814	1738
Missense (PolyPhen)		48	48.035	0.99927		610
Synonymous	-2.04	85	64.2	1.32	0.00000390	580
Loss of Function	0.537	8	9.82	0.815	4.18e-7	132

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00040	0.00038	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Hydrolase acting on ester bonds. {ECO:0000305}.;

Recessive Scores

pRec: 0.0964

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.171

Gene Damage Prediction

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