PHACTR2

protein-coding

phosphatase and actin regulator 2, the group of Phosphatase and actin regulators

Gene summary

Predicted to enable actin binding activity. Predicted to be involved in actin cytoskeleton organization. Predicted to be located in plasma membrane and platelet alpha granule membrane. Implicated in Parkinson's disease and multiple sclerosis. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf56

MANE transcript

NM_001100164.2

Inheritance

ClinVar variants

U:102B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr6:143,536,845-143,831,185

External References & Databases

Ensembl (ENSG00000112419)

Transcript & Mutation Effects

hg38 • Region Span ~294.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

dilated cardiomyopathyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0005021

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PHACTR2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 99

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001100164.2. 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			98 clinvar	3 clinvar		101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	102	4	0	106

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001100164.2	RefSeq	NP_001093634.1	13	MANE Select
ENST00000440869.7	Ensembl	ENSP00000417038.2	13	MANE Select
NM_001100165.2	RefSeq	NP_001093635.1	12	Standard
NM_001100166.2	RefSeq	NP_001093636.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet degranulation
Response to elevated platelet cytosolic Ca2+
Platelet activation, signaling and aggregation
Hemostasis

Biological Process

platelet degranulation
negative regulation of phosphoprotein phosphatase activity

Molecular Function

actin binding
protein phosphatase inhibitor activity
protein binding

Cellular Component

plasma membrane
platelet alpha granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000440869
Coding exons: 13
Length: 294341
Individuals with no LoFs: 124759
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 124792
p: 0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.813	299	341	0.876	0.0000184	4142
Missense (PolyPhen)		120	174.46	0.68784		2211
Synonymous	-0.234	136	133	1.03	0.00000777	1315
Loss of Function	3.01	16	35.3	0.454	0.00000234	388

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0917

Intolerance Scores

LoFtool: 0.858
RVIS EVS: -0.05
RVIS percentile EVS: 50.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00879

Gene Damage Prediction

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