HAGHL

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

Basic information

Region (hg38): 16:726936-735525

Links

ENSG00000103253 ∙ NCBI:84264 ∙ ∙ HGNC:14177 ∙ Uniprot:Q6PII5 ∙ 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 HAGHL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAGHL 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in HAGHL

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

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

Position	Type	Phenotype	Significance	ClinVar
16-727531-G-C		not specified	Uncertain significance (Mar 28, 2023)
16-727567-G-A		not specified	Uncertain significance (Aug 26, 2022)
16-727596-C-A		not specified	Uncertain significance (Mar 28, 2023)
16-727996-C-T		not specified	Uncertain significance (May 20, 2024)
16-728117-G-A		not specified	Uncertain significance (Oct 10, 2023)
16-728135-C-G		not specified	Likely benign (Jul 11, 2023)
16-728172-T-C		not specified	Uncertain significance (Apr 04, 2024)
16-728181-A-C		not specified	Uncertain significance (Mar 01, 2023)
16-728181-A-G		not specified	Uncertain significance (Apr 11, 2023)
16-728199-T-C		not specified	Uncertain significance (Apr 20, 2024)
16-728325-A-G		not specified	Uncertain significance (Feb 13, 2023)
16-728330-C-A		not specified	Uncertain significance (Sep 20, 2023)
16-728516-C-G		not specified	Uncertain significance (Feb 03, 2022)
16-728534-C-G		not specified	Uncertain significance (Jan 19, 2024)
16-728537-G-T		not specified	Uncertain significance (Jun 07, 2024)
16-728804-G-A		not specified	Uncertain significance (Apr 18, 2023)
16-728809-C-T		not specified	Uncertain significance (Oct 10, 2023)
16-728834-A-C		not specified	Uncertain significance (Apr 18, 2023)
16-728869-G-A		not specified	Uncertain significance (Jun 17, 2022)
16-728887-T-C		not specified	Uncertain significance (May 10, 2024)
16-729027-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-729049-T-C		not specified	Uncertain significance (Sep 20, 2023)
16-729057-G-A		not specified	Uncertain significance (Dec 11, 2023)
16-729313-G-A		not specified	Uncertain significance (Sep 14, 2022)
16-729325-C-A		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAGHL	protein_coding	protein_coding	ENST00000389703	8	8590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000198	0.484	124748	0	15	124763	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.724	166	142	1.17	0.00000814	1738
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000630	0.0000623
Ashkenazi Jewish	0.00	0.00
East Asian	0.000398	0.000382
Finnish	0.00	0.00
European (Non-Finnish)	0.0000561	0.0000534
Middle Eastern	0.000398	0.000382
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolase acting on ester bonds. {ECO:0000305}.
• Pathway: Pyruvate metabolism (Consensus)

Recessive Scores

• pRec: 0.0964

Haploinsufficiency Scores

• pHI: 0.0652
• hipred: N
• hipred_score: 0.322
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Haghl

Gene ontology

• Molecular function: hydrolase activity;metal ion binding