GeneBe

ACP6

acid phosphatase 6, lysophosphatidic, the group of Acid phosphatases

Basic information

Region (hg38): 1:147629652-147670524

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.

  • not_specified (59 variants)
  • not_provided (3 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. These statistics are base on transcript: NM_000016361.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
1
clinvar
53
clinvar
5
clinvar
2
clinvar
 61
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 1 53 5 3

Highest pathogenic variant AF is 0.000898891

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ACP6protein_codingprotein_codingENST00000369238 1041166
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.33e-130.03471256820661257480.000262
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6782062350.8760.00001172791
Missense in Polyphen5150.8691.0026537
Synonymous0.7848796.80.8990.00000525816
Loss of Function0.1932021.00.9558.92e-7249

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005520.000536
Ashkenazi Jewish0.000.00
East Asian0.0007110.000707
Finnish0.00004620.0000462
European (Non-Finnish)0.0001870.000185
Middle Eastern0.0007110.000707
South Asian0.0004910.000490
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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