ACP4

acid phosphatase 4, the group of Acid phosphatases

Basic information

Region (hg38): 19:50790415-50795219

Previous symbols: [ "ACPT" ]

Links

ENSG00000142513 ∙ NCBI:93650 ∙ OMIM:606362 ∙ HGNC:14376 ∙ Uniprot:Q9BZG2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amelogenesis imperfecta type 1 (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, type IJ	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dental	27843125

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACP4 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				5	1	6
missense		2	34		3	39
nonsense			1			1
start loss						0
frameshift		1				1
inframe indel					1	1
splice donor/acceptor (+/-2bp)		1		1		2
splice region				3	1	4
non coding					1	1
Total	0	4	35	6	6

Variants in ACP4

This is a list of pathogenic ClinVar variants found in the ACP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50790421-G-A		not specified	Uncertain significance (Aug 10, 2024)
19-50790456-CCTG-C		ACP4-related disorder	Benign (Aug 15, 2019)
19-50790487-C-T		not specified	Uncertain significance (Apr 26, 2023)
19-50790517-G-A		not specified	Uncertain significance (Mar 23, 2023)
19-50790601-G-A		not specified	Uncertain significance (Dec 14, 2021)
19-50790612-C-T		not specified	Uncertain significance (Sep 22, 2023)
19-50790619-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-50790620-G-A		ACP4-related disorder	Likely benign (Feb 25, 2019)
19-50790676-G-A		not specified	Uncertain significance (Nov 11, 2024)
19-50790697-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-50790698-G-A		ACP4-related disorder	Benign (Jan 20, 2020)
19-50790783-C-T		Amelogenesis imperfecta, type 1J	Pathogenic (Aug 15, 2019)
19-50790784-G-A		not specified	Uncertain significance (May 30, 2023)
19-50790784-GCCAGCAGCTGGAGCTGG-A			Likely pathogenic (Dec 20, 2022)
19-50790819-C-A		Amelogenesis imperfecta	Uncertain significance (Feb 03, 2021)
19-50790849-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-50790850-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-50791666-G-A		not specified	Uncertain significance (Nov 17, 2022)
19-50791683-C-T		Amelogenesis imperfecta, type 1J	Likely pathogenic (Dec 20, 2022)
19-50791702-A-G		Amelogenesis imperfecta • not specified	Uncertain significance (Jan 04, 2022)
19-50791715-C-T		ACP4-related disorder	Likely benign (Feb 21, 2019)
19-50791727-C-T			Benign (Dec 31, 2019)
19-50791734-G-C		Amelogenesis imperfecta, type 1J	Pathogenic (Aug 15, 2019)
19-50791749-G-A		Amelogenesis imperfecta, type 1J	Pathogenic (Aug 15, 2019)
19-50791762-G-C		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACP4	protein_coding	protein_coding	ENST00000270593	11	4810

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.62e-15	0.00967	125645	0	102	125747	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.131	265	271	0.978	0.0000171	2626
Missense in Polyphen		104	125.05	0.83164		1225
Synonymous	-0.980	135	121	1.11	0.00000737	970
Loss of Function	-0.216	21	20.0	1.05	9.40e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000825	0.000814
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000610	0.000598
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000349	0.000343
Middle Eastern	0.000610	0.000598
South Asian	0.00102	0.00101
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May dephosphorylate receptor tyrosine-protein kinase ERBB4 and inhibits its ligand-induced proteolytic cleavage (PubMed:15219672). May play a role in odontogenesis (PubMed:27843125). {ECO:0000269|PubMed:15219672, ECO:0000269|PubMed:27843125}.
• Disease: DISEASE: Amelogenesis imperfecta 1J (AI1J) [MIM:617297]: A form of amelogenesis imperfecta, a disorder characterized by defective enamel formation. The enamel may be hypoplastic, hypomineralized or both, and affected teeth may be discoloured, sensitive or prone to disintegration. AI1J is an autosomal recessive form characterized by hypoplastic enamel, enamel discolorization ranging from yellow to black, and normal dentin. {ECO:0000269|PubMed:27843125}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.277

Intolerance Scores

• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.170
• ghis: 0.431

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Acp4

Gene ontology

• Biological process: negative regulation of protein processing;negative regulation of neuron projection development;odontogenesis;regulation of neuronal synaptic plasticity;negative regulation of ERBB4 signaling pathway;peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity
• Cellular component: integral component of membrane;postsynaptic membrane
• Molecular function: acid phosphatase activity;protein tyrosine phosphatase activity;receptor tyrosine kinase binding