PSTPIP2

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

Basic information

Region (hg38): 18:45983536-46072272

Links

ENSG00000152229

∙ NCBI:9050 ∙ OMIM:616046 ∙ HGNC:9581 ∙ Uniprot:Q9H939 ∙ 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 PSTPIP2 gene.

not_specified (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSTPIP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024430.4. 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			3 clinvar			3
missense			21 clinvar	1 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	26	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSTPIP2	protein_coding	protein_coding	ENST00000409746	14	88737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00280	0.997	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	137	180	0.761	0.00000960	2223
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000284	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000501	0.0000462
European (Non-Finnish)	0.0000892	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

pHI: 0.0845
hipred: Y
hipred_score: 0.718
ghis: 0.401

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pstpip2
Phenotype: cellular phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear 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); hematopoietic system phenotype;

Gene ontology

Biological process: cell migration;actin filament polymerization
Cellular component: cytoplasm;cytosol;cytoskeleton;actin filament;plasma membrane
Molecular function: cytoskeletal protein binding;actin filament binding