ACYP2

acylphosphatase 2

Basic information

Region (hg38): 2:53970837-54305300

Links

ENSG00000170634 ∙ NCBI:98 ∙ OMIM:102595 ∙ HGNC:180 ∙ Uniprot:P14621 ∙ 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 ACYP2 gene.

• Inborn genetic diseases (24 variants)
• not provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACYP2 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			18	5	11	34
Total	0	0	22	5	11

Variants in ACYP2

This is a list of pathogenic ClinVar variants found in the ACYP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-54057304-G-A			Benign (Jan 17, 2024)
2-54115733-A-T		not specified	Uncertain significance (May 11, 2022)
2-54138665-A-G		not specified	Uncertain significance (Aug 09, 2021)
2-54138675-G-A		not specified	Uncertain significance (Feb 28, 2024)
2-54138705-G-A		not specified	Uncertain significance (Nov 30, 2022)
2-54248729-C-A		Chronic osteomyelitis	association (Sep 01, 2016)
2-54254983-G-A		not specified	Uncertain significance (Apr 17, 2023)
2-54255130-T-C		not specified	Uncertain significance (Sep 14, 2023)
2-54255157-C-T		not specified	Likely benign (Feb 28, 2023)
2-54255162-C-A		not specified	Uncertain significance (Oct 14, 2023)
2-54255197-C-A		not specified	Uncertain significance (Feb 05, 2024)
2-54255254-T-C		not specified	Uncertain significance (Nov 13, 2023)
2-54255267-C-G		not specified	Uncertain significance (Jul 05, 2022)
2-54255301-T-A		not specified	Uncertain significance (Feb 13, 2024)
2-54255309-T-G		not specified	Uncertain significance (Jul 26, 2022)
2-54255336-C-G		not specified	Uncertain significance (Jan 03, 2024)
2-54255357-C-G		not specified	Uncertain significance (Sep 26, 2023)
2-54255518-G-C		not specified	Uncertain significance (Feb 17, 2022)
2-54255566-GGGGCCC-G			Benign (Dec 31, 2019)
2-54255569-G-A		not specified	Uncertain significance (Jun 28, 2023)
2-54255574-G-A		not specified	Uncertain significance (Aug 21, 2023)
2-54255600-G-C		not specified	Likely benign (Feb 23, 2023)
2-54255616-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-54255705-G-A			Benign (Dec 31, 2019)
2-54255724-G-A		not specified	Uncertain significance (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACYP2	protein_coding	protein_coding	ENST00000394666	4	334463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000653	0.298	125718	0	27	125745	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.512	63	52.5	1.20	0.00000257	647
Missense in Polyphen		16	17.923	0.89269		204
Synonymous	-0.951	23	17.9	1.29	8.84e-7	181
Loss of Function	-0.207	6	5.48	1.10	2.32e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00100	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.0000710	0.0000703
Middle Eastern	0.00100	0.000979
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Its physiological role is not yet clear.
• Pathway: Pyruvate metabolism - Homo sapiens (human);Pyruvate metabolism (Consensus)

Recessive Scores

• pRec: 0.202

Intolerance Scores

• loftool: 0.507
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.251
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acyp2

Gene ontology

• Biological process: phosphate-containing compound metabolic process
• Molecular function: acylphosphatase activity;protein binding;identical protein binding