HAGH

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

Basic information

Region (hg38): 16:1795620-1827157

Links

ENSG00000063854 ∙ NCBI:3029 ∙ OMIM:138760 ∙ HGNC:4805 ∙ Uniprot:Q16775 ∙ 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 HAGH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAGH 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in HAGH

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

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

Position	Type	Phenotype	Significance	ClinVar
16-1809290-C-T		not specified	Uncertain significance (Dec 22, 2023)
16-1809299-T-C		not specified	Uncertain significance (Aug 05, 2024)
16-1809303-A-G		not specified	Uncertain significance (Jul 31, 2024)
16-1809312-T-C		not specified	Uncertain significance (Sep 01, 2024)
16-1809360-C-T		not specified	Uncertain significance (Mar 28, 2023)
16-1809791-C-T		not specified	Uncertain significance (Oct 12, 2024)
16-1809797-T-C		not specified	Uncertain significance (Jun 22, 2024)
16-1809818-C-T		not specified	Uncertain significance (Aug 07, 2024)
16-1809827-A-T		not specified	Uncertain significance (Feb 07, 2023)
16-1816916-G-A		not specified	Uncertain significance (Apr 01, 2024)
16-1816927-T-C		not specified	Uncertain significance (Feb 05, 2024)
16-1816940-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-1816945-C-T		not specified	Uncertain significance (Jun 02, 2024)
16-1816981-C-T		not specified	Uncertain significance (Sep 05, 2024)
16-1816985-A-G		not specified	Uncertain significance (Oct 14, 2023)
16-1817250-C-A		not specified	Uncertain significance (Nov 12, 2024)
16-1817253-G-A		not specified	Uncertain significance (Jun 09, 2022)
16-1819189-G-T		not specified	Uncertain significance (Sep 14, 2022)
16-1819190-G-A		not specified	Uncertain significance (Apr 17, 2024)
16-1819208-C-T		not specified	Uncertain significance (Dec 30, 2023)
16-1819898-T-G		not specified	Uncertain significance (Aug 08, 2023)
16-1819920-T-C		not specified	Likely benign (Aug 19, 2023)
16-1819952-C-A		not specified	Uncertain significance (Aug 11, 2024)
16-1819952-C-T		not specified	Uncertain significance (Nov 20, 2024)
16-1822340-C-T		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAGH	protein_coding	protein_coding	ENST00000397356	9	31575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000177	0.899	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.12	233	190	1.23	0.0000124	1973
Missense in Polyphen		88	72.046	1.2214		728
Synonymous	-1.92	107	84.5	1.27	0.00000628	638
Loss of Function	1.49	8	14.0	0.571	5.89e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000489	0.000489
Ashkenazi Jewish	0.000795	0.000794
East Asian	0.00	0.00
Finnish	0.000213	0.000185
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid.
• Pathway: Pyruvate metabolism - Homo sapiens (human);Pyruvate Dehydrogenase Complex Deficiency;Primary hyperoxaluria II, PH2;Pyruvate kinase deficiency;Leigh Syndrome;Pyruvate Metabolism;Pyruvate Decarboxylase E1 Component Deficiency (PDHE1 Deficiency);Pyruvaldehyde Degradation;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;p73 transcription factor network;Pyruvate metabolism;methylglyoxal degradation I (Consensus)

Recessive Scores

• pRec: 0.301

Intolerance Scores

• loftool: 0.160
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.324
• hipred: N
• hipred_score: 0.294
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hagh

Gene ontology

• Biological process: pyruvate metabolic process;glutathione biosynthetic process;methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione
• Cellular component: mitochondrial matrix;cytosol
• Molecular function: hydroxyacylglutathione hydrolase activity;protein binding;metal ion binding