PHACTR4

phosphatase and actin regulator 4, the group of Protein phosphatase 1 regulatory subunits|Phosphatase and actin regulators

Basic information

Region (hg38): 1:28369581-28500364

Links

ENSG00000204138 ∙ NCBI:65979 ∙ OMIM:608726 ∙ HGNC:25793 ∙ Uniprot:Q8IZ21 ∙ 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 PHACTR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHACTR4 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			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	30	3	0

Variants in PHACTR4

This is a list of pathogenic ClinVar variants found in the PHACTR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-28438421-G-A		not specified	Uncertain significance (Jul 08, 2022)
1-28459110-G-T		not specified	Likely benign (Nov 28, 2023)
1-28459156-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-28459159-A-C		not specified	Uncertain significance (Jun 23, 2023)
1-28459169-A-G		not specified	Uncertain significance (Aug 17, 2022)
1-28459189-G-T		not specified	Uncertain significance (Jan 23, 2023)
1-28459219-A-G		not specified	Uncertain significance (Jan 18, 2022)
1-28460220-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-28465697-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-28465727-A-G		not specified	Uncertain significance (Jun 11, 2021)
1-28465769-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-28466466-C-T		not specified	Uncertain significance (Jan 31, 2024)
1-28466543-A-C		not specified	Uncertain significance (Jul 14, 2021)
1-28466558-A-G		not specified	Uncertain significance (Jun 16, 2024)
1-28466690-C-G		not specified	Uncertain significance (Mar 29, 2024)
1-28466738-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-28466745-A-T		not specified	Uncertain significance (Oct 27, 2022)
1-28473556-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-28473578-G-C		not specified	Uncertain significance (Jul 13, 2022)
1-28473598-C-G		not specified	Uncertain significance (Nov 12, 2021)
1-28473599-C-T		not specified	Uncertain significance (Feb 11, 2022)
1-28473607-C-A		not specified	Uncertain significance (Jul 13, 2022)
1-28473629-T-C		not specified	Uncertain significance (Mar 07, 2023)
1-28473710-C-T		not specified	Uncertain significance (Jul 26, 2021)
1-28473718-A-G		not specified	Likely benign (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHACTR4	protein_coding	protein_coding	ENST00000373836	13	130768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000284	0.999	124775	1	34	124810	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	334	396	0.844	0.0000212	4635
Missense in Polyphen		103	137.67	0.74814		1599
Synonymous	0.987	126	141	0.894	0.00000750	1429
Loss of Function	2.97	15	33.5	0.447	0.00000202	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000285	0.000285
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000168
Middle Eastern	0.000111	0.000111
South Asian	0.000164	0.000131
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of protein phosphatase 1 (PP1) required for neural tube and optic fissure closure, and enteric neural crest cell (ENCCs) migration during development. Acts as an activator of PP1 by interacting with PPP1CA and preventing phosphorylation of PPP1CA at 'Thr-320'. During neural tube closure, localizes to the ventral neural tube and activates PP1, leading to down-regulate cell proliferation within cranial neural tissue and the neural retina. Also acts as a regulator of migration of enteric neural crest cells (ENCCs) by activating PP1, leading to dephosphorylation and subsequent activation of cofilin (COF1 or COF2) and repression of the integrin signaling through the RHO/ROCK pathway (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0662

Intolerance Scores

• loftool: 0.862
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.53

Haploinsufficiency Scores

• pHI: 0.0406
• hipred: N
• hipred_score: 0.379
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.202

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phactr4
• Phenotype: cellular phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); pigmentation phenotype; embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: neural crest cell migration;neural tube closure;Rho protein signal transduction;actin cytoskeleton organization;positive regulation of catalytic activity;regulation of phosphoprotein phosphatase activity;enteric nervous system development;regulation of cell cycle;closure of optic fissure;negative regulation of integrin-mediated signaling pathway
• Cellular component: cytoplasm;lamellipodium
• Molecular function: actin binding;protein phosphatase 1 binding;protein phosphatase activator activity