CHAC2

ChaC glutathione specific gamma-glutamylcyclotransferase 2

Basic information

Region (hg38): 2:53767804-53775196

Links

ENSG00000143942 ∙ NCBI:494143 ∙ OMIM:617446 ∙ HGNC:32363 ∙ Uniprot:Q8WUX2 ∙ 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 CHAC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHAC2 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in CHAC2

This is a list of pathogenic ClinVar variants found in the CHAC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-53767892-G-C		not specified	Uncertain significance (May 11, 2022)
2-53767905-G-C		not specified	Uncertain significance (Jun 29, 2022)
2-53767924-T-C		not specified	Uncertain significance (Oct 30, 2023)
2-53767947-C-G		not specified	Uncertain significance (Sep 13, 2023)
2-53767963-C-T		not specified	Uncertain significance (Nov 20, 2023)
2-53767983-T-C		not specified	Uncertain significance (May 20, 2024)
2-53767990-G-A		not specified	Uncertain significance (Jan 30, 2024)
2-53767992-A-C		not specified	Uncertain significance (Dec 18, 2023)
2-53767993-G-C		not specified	Uncertain significance (Nov 20, 2023)
2-53767994-C-G		not specified	Uncertain significance (Feb 28, 2023)
2-53774160-G-A		not specified	Uncertain significance (Sep 28, 2022)
2-53774182-A-G		not specified	Uncertain significance (Oct 30, 2023)
2-53774193-G-A		not specified	Uncertain significance (Jun 01, 2023)
2-53774281-T-G		not specified	Uncertain significance (Nov 30, 2022)
2-53774317-C-G		not specified	Uncertain significance (Dec 26, 2023)
2-53774350-T-C		not specified	Uncertain significance (Jun 07, 2023)
2-53774359-A-G		not specified	Uncertain significance (Dec 14, 2021)
2-53774407-T-C		not specified	Uncertain significance (Jun 18, 2021)
2-53774416-C-G		not specified	Uncertain significance (Apr 13, 2022)
2-53774424-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-53774452-A-T		not specified	Uncertain significance (May 02, 2024)
2-53774508-A-C		not specified	Uncertain significance (Jan 03, 2024)
2-53774511-C-T		not specified	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHAC2	protein_coding	protein_coding	ENST00000295304	3	7405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000229	0.165	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.18	131	98.0	1.34	0.00000456	1193
Missense in Polyphen		43	32.143	1.3378		396
Synonymous	-1.28	44	34.4	1.28	0.00000156	354
Loss of Function	-0.382	8	6.92	1.16	2.89e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000549	0.000539
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000617	0.000615
Middle Eastern	0.000164	0.000163
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the cleavage of glutathione into 5-oxo-L- proline and a Cys-Gly dipeptide. Acts specifically on glutathione, but not on other gamma-glutamyl peptides. {ECO:0000269|PubMed:27913623}.
• Pathway: Glutathione conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Glutathione synthesis and recycling (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.735
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.0970
• hipred: N
• hipred_score: 0.468
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chac2

Gene ontology

• Biological process: glutathione biosynthetic process;glutathione catabolic process;biological_process
• Cellular component: cellular_component;cytoplasm;cytosol
• Molecular function: molecular_function;gamma-glutamylcyclotransferase activity;glutathione specific gamma-glutamylcyclotransferase activity