PHACTR4

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

Basic information

Region (hg38): 1:28369582-28500364

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.

not_specified (87 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_001048183.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			81 clinvar	5 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	81	5	0

Loading clinvar variants...

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