ACP6

acid phosphatase 6, lysophosphatidic, the group of Acid phosphatases

Basic information

Region (hg38): 1:147629651-147670524

Links

ENSG00000162836 ∙ NCBI:51205 ∙ OMIM:611471 ∙ HGNC:29609 ∙ Uniprot:Q9NPH0 ∙ 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 ACP6 gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)
• not specified (1 variants)
• Cerebral visual impairment and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACP6 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					1	1
missense		1	17	4	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	17	4	3

Highest pathogenic variant AF is 0.000440

Variants in ACP6

This is a list of pathogenic ClinVar variants found in the ACP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-147647445-A-G		not specified	Uncertain significance (May 16, 2022)
1-147647504-C-T		not specified	Uncertain significance (Apr 17, 2023)
1-147647506-T-C			Benign (Nov 20, 2018)
1-147648251-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-147648270-A-T		not specified	Uncertain significance (Feb 23, 2023)
1-147648276-C-A		not specified	Uncertain significance (Aug 12, 2021)
1-147650153-C-T		not specified	Likely benign (Mar 07, 2023)
1-147654205-C-T		not specified	Uncertain significance (Jun 05, 2023)
1-147654208-C-T		not specified	Likely benign (Oct 26, 2022)
1-147654241-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-147654262-T-C		not specified	Likely benign (Sep 26, 2022)
1-147654301-G-C		not specified	Uncertain significance (Oct 29, 2021)
1-147654302-T-C			Benign (Nov 20, 2018)
1-147654314-C-G		not specified	Uncertain significance (Jul 20, 2021)
1-147654322-G-A		not specified	Benign (Mar 06, 2015)
1-147655173-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-147655201-G-A		not specified	Uncertain significance (Oct 30, 2023)
1-147655209-A-C		not specified	Uncertain significance (Nov 27, 2023)
1-147655223-T-G		not specified	Uncertain significance (Mar 20, 2023)
1-147659017-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-147659415-A-T		not specified	Uncertain significance (Oct 25, 2022)
1-147659466-C-T		not specified	Uncertain significance (Dec 17, 2021)
1-147659496-C-T		Cerebral visual impairment and intellectual disability	Likely pathogenic (Sep 09, 2015)
1-147659517-A-T		not specified	Uncertain significance (Mar 04, 2024)
1-147659522-C-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACP6	protein_coding	protein_coding	ENST00000369238	10	41166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.33e-13	0.0347	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	206	235	0.876	0.0000117	2791
Missense in Polyphen		51	50.869	1.0026		537
Synonymous	0.784	87	96.8	0.899	0.00000525	816
Loss of Function	0.193	20	21.0	0.955	8.92e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000552	0.000536
Ashkenazi Jewish	0.00	0.00
East Asian	0.000711	0.000707
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000711	0.000707
South Asian	0.000491	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes lysophosphatidic acid (LPA) containing a medium length fatty acid chain to the corresponding monoacylglycerol. Has highest activity with lysophosphatidic acid containing myristate (C14:0), monounsaturated oleate (C18:1) or palmitate (C16:0), and lower activity with C18:0 and C6:0 lysophosphatidic acid. {ECO:0000269|PubMed:10506173, ECO:0000269|PubMed:23807634}.
• Pathway: Vitamin B2 (riboflavin) metabolism;Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.822
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.74

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.170
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.594

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acp6
• Phenotype: normal phenotype

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;phospholipid metabolic process;phosphatidic acid biosynthetic process;dephosphorylation;lysobisphosphatidic acid metabolic process
• Cellular component: cytoplasm;mitochondrion;mitochondrial matrix
• Molecular function: acid phosphatase activity;lysophosphatidic acid phosphatase activity