PSTPIP2

protein-coding

proline-serine-threonine phosphatase interacting protein 2, the group of F-BAR domain containing

Gene summary

Predicted to be located in cytoskeleton; cytosol; and membrane. Predicted to be active in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024430.4

Inheritance

—

ClinVar variants

U:29B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr18:45,983,536-46,072,272

External References & Databases

Ensembl (ENSG00000152229)

Transcript & Mutation Effects

hg38 • Region Span ~88.7 kb

Loading mutation effect viewer...

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 PSTPIP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 27

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024430.4. 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			3 clinvar			3
missense			24 clinvar	3 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	29	3	0	32

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024430.4	RefSeq	NP_077748.3	14	MANE Select
ENST00000409746.5	Ensembl	ENSP00000387261.4	14	MANE Select
ENST00000589328.5	Ensembl	ENSP00000468622.1	14	Standard
ENST00000589328.6	Ensembl	ENSP00000468622.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell migration
actin filament polymerization

Molecular Function

cytoskeletal protein binding
actin filament binding

Cellular Component

cytoplasm
cytosol
cytoskeleton
actin filament
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409746
Coding exons: 14
Length: 88737
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125748
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	137	180	0.761	0.00000960	2223
Missense (PolyPhen)		26	51.901	0.50095		629
Synonymous	0.144	60	61.4	0.977	0.00000322	544
Loss of Function	3.38	10	29.9	0.334	0.00000182	313

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to F-actin. May be involved in regulation of the actin cytoskeleton (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0846

Intolerance Scores

LoFtool: 0.630
RVIS EVS: 0.06
RVIS percentile EVS: 58.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.165

Gene Damage Prediction

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