ACY3

aminoacylase 3

Basic information

Region (hg38): 11:67642554-67650730

Links

ENSG00000132744 ∙ NCBI:91703 ∙ OMIM:614413 ∙ HGNC:24104 ∙ Uniprot:Q96HD9 ∙ 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 ACY3 gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACY3 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			21	1		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	21	1	0

Variants in ACY3

This is a list of pathogenic ClinVar variants found in the ACY3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67642755-G-A		not specified	Likely benign (Dec 27, 2023)
11-67642756-C-A		not specified	Uncertain significance (Feb 28, 2023)
11-67642783-A-G		not specified	Likely benign (Mar 16, 2022)
11-67642840-A-T		not specified	Uncertain significance (Apr 25, 2022)
11-67642867-C-T		not specified	Uncertain significance (May 27, 2022)
11-67642879-C-T		not specified	Uncertain significance (Jul 30, 2023)
11-67642902-A-G		not specified	Uncertain significance (Jul 19, 2022)
11-67642932-T-A		not specified	Uncertain significance (Jun 27, 2022)
11-67644822-C-T		not specified	Uncertain significance (May 09, 2023)
11-67645062-A-G		not specified	Uncertain significance (Sep 14, 2022)
11-67645094-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-67645337-C-T		not specified	Uncertain significance (Jan 16, 2024)
11-67645344-A-G		not specified	Uncertain significance (May 17, 2023)
11-67645358-C-G		not specified	Uncertain significance (Nov 18, 2022)
11-67645706-A-T		not specified	Uncertain significance (Feb 15, 2023)
11-67645810-G-A		not specified	Uncertain significance (Jul 30, 2023)
11-67645822-C-T		not specified	Uncertain significance (Oct 29, 2021)
11-67645856-C-T		not specified	Uncertain significance (Sep 29, 2022)
11-67645870-T-C		not specified	Uncertain significance (Oct 12, 2021)
11-67646833-G-A		not specified	Uncertain significance (Aug 17, 2022)
11-67646860-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-67646882-G-C		not specified	Uncertain significance (Aug 12, 2021)
11-67646887-C-T		not specified	Uncertain significance (Feb 03, 2022)
11-67646950-G-A		not specified	Uncertain significance (Oct 29, 2021)
11-67646997-A-G		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACY3	protein_coding	protein_coding	ENST00000255082	6	8105

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000542	0.446	125720	0	23	125743	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0585	200	198	1.01	0.0000124	2029
Missense in Polyphen		52	53.057	0.98007		646
Synonymous	0.659	83	91.0	0.912	0.00000636	678
Loss of Function	0.551	9	11.0	0.820	5.53e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000332	0.000331
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000476	0.0000462
European (Non-Finnish)	0.0000984	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in deacetylating mercapturic acids in kidney proximal tubules. Also acts on N-acetyl-aromatic amino acids (By similarity). {ECO:0000250}.
• Pathway: Biological oxidations;Metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aflatoxin activation and detoxification (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.269
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.17

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.889

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acy3

Gene ontology

• Biological process: xenobiotic metabolic process;biological_process;viral process
• Cellular component: cytosol;apical plasma membrane;extracellular exosome
• Molecular function: molecular_function;aminoacylase activity;protein binding;hydrolase activity, acting on ester bonds;identical protein binding;metal ion binding