PHACTR3

protein-coding

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

Gene summary

This gene encodes a member of the phosphatase and actin regulator protein family. The encoded protein is associated with the nuclear scaffold in proliferating cells, and binds to actin and the catalytic subunit of protein phosphatase-1, suggesting that it functions as a regulatory subunit of protein phosphatase-1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Previous symbols:

C20orf101

MANE transcript

NM_080672.5

Inheritance

—

ClinVar variants

U:74B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr20:59,577,509-59,847,711

External References & Databases

Ensembl (ENSG00000087495)

Transcript & Mutation Effects

hg38 • Region Span ~270.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PHACTR3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080672.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			71 clinvar	1 clinvar		72
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	74	1	0	75

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080672.5	RefSeq	NP_542403.1	13	MANE Select
ENST00000371015.6	Ensembl	ENSP00000360054.1	13	MANE Select
NM_001199505.1	RefSeq	NP_001186434.1	13	Standard
NM_001199506.2	RefSeq	NP_001186435.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of phosphoprotein phosphatase activity

Molecular Function

actin binding
protein phosphatase inhibitor activity
protein phosphatase 1 binding

Cellular Component

nucleoplasm
nuclear matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371015
Coding exons: 13
Length: 270203
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.972	268	317	0.846	0.0000195	3618
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.518
RVIS EVS: -0.22
RVIS percentile EVS: 37.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.959

Gene Damage Prediction

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