PHACTR3

phosphatase and actin regulator 3, the group of Protein phosphatase 1 regulatory subunits|Phosphatase and actin regulators

Basic information

Region (hg38): 20:59577509-59847711

Previous symbols: [ "C20orf101" ]

Links

ENSG00000087495 ∙ NCBI:116154 ∙ OMIM:608725 ∙ HGNC:15833 ∙ Uniprot:Q96KR7 ∙ 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 PHACTR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHACTR3 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			48	1		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	1	0

Variants in PHACTR3

This is a list of pathogenic ClinVar variants found in the PHACTR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-59577524-G-T		not specified	Uncertain significance (Aug 09, 2021)
20-59577527-G-T		not specified	Uncertain significance (Oct 14, 2021)
20-59577579-C-T		not specified	Uncertain significance (Jun 21, 2021)
20-59605025-C-G		not specified	Uncertain significance (Nov 21, 2023)
20-59605045-C-G		not specified	Uncertain significance (Apr 08, 2024)
20-59605061-G-T		not specified	Uncertain significance (Dec 25, 2024)
20-59605096-T-G		not specified	Uncertain significance (Oct 12, 2022)
20-59743155-G-T		not specified	Uncertain significance (Apr 23, 2024)
20-59743206-G-A		not specified	Uncertain significance (Mar 01, 2025)
20-59743241-A-G		not specified	Uncertain significance (Apr 01, 2024)
20-59747778-G-A		not specified	Uncertain significance (Dec 28, 2023)
20-59747791-G-A		not specified	Uncertain significance (Mar 04, 2024)
20-59755208-G-A		not specified	Uncertain significance (Mar 08, 2025)
20-59755232-A-G		not specified	Uncertain significance (Jan 16, 2025)
20-59755238-C-T		not specified	Uncertain significance (Jun 21, 2022)
20-59755280-C-A		not specified	Uncertain significance (May 14, 2024)
20-59755286-G-C		not specified	Uncertain significance (Aug 27, 2024)
20-59755298-G-C		not specified	Uncertain significance (Feb 01, 2025)
20-59767194-C-A		not specified	Uncertain significance (Oct 26, 2022)
20-59767210-G-A		not specified	Uncertain significance (Feb 28, 2023)
20-59767249-A-G		not specified	Uncertain significance (Dec 04, 2024)
20-59767258-C-G		not specified	Uncertain significance (Mar 10, 2025)
20-59767275-G-A		not specified	Uncertain significance (Jul 25, 2024)
20-59767290-A-G		not specified	Uncertain significance (Oct 25, 2023)
20-59767334-C-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHACTR3	protein_coding	protein_coding	ENST00000371015	13	270203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00313	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.972	268	317	0.846	0.0000195	3618
Missense in Polyphen		75	121.8	0.61575		1269
Synonymous	-1.41	152	131	1.16	0.00000866	1103
Loss of Function	4.59	3	30.2	0.0994	0.00000185	340

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.518
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.6

Haploinsufficiency Scores

• pHI: 0.428
• hipred: Y
• hipred_score: 0.798
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phactr3

Gene ontology

• Biological process: negative regulation of phosphoprotein phosphatase activity
• Cellular component: nucleoplasm;nuclear matrix
• Molecular function: actin binding;protein phosphatase inhibitor activity;protein phosphatase 1 binding