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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14	1		15
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in PSTPIP2

This is a list of pathogenic ClinVar variants found in the PSTPIP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
18-45990746-G-C		not specified	Uncertain significance (Oct 12, 2021)
18-45990755-T-C		not specified	Uncertain significance (Jan 01, 2025)
18-45991906-C-T		not specified	Uncertain significance (Aug 04, 2024)
18-45991918-C-T		not specified	Uncertain significance (Jul 09, 2021)
18-45991974-A-G		not specified	Uncertain significance (Feb 13, 2025)
18-45992129-C-T		not specified	Uncertain significance (Feb 24, 2025)
18-45992150-A-G		not specified	Uncertain significance (Aug 08, 2023)
18-45993645-T-C		not specified	Uncertain significance (Jun 05, 2024)
18-45993703-C-T		not specified	Uncertain significance (Jul 09, 2021)
18-45998796-G-A		not specified	Uncertain significance (Feb 25, 2025)
18-45999461-A-T		not specified	Uncertain significance (Oct 05, 2023)
18-45999506-C-T		not specified	Uncertain significance (Jun 02, 2024)
18-46011201-G-C		not specified	Uncertain significance (Apr 14, 2023)
18-46011215-T-A		not specified	Uncertain significance (Mar 06, 2023)
18-46011278-T-C		not specified	Likely benign (Oct 12, 2021)
18-46015924-C-A		not specified	Uncertain significance (Oct 27, 2023)
18-46039986-C-A		not specified	Uncertain significance (Mar 18, 2024)
18-46040038-T-A		not specified	Uncertain significance (Jan 31, 2023)
18-46072166-C-T		not specified	Uncertain significance (Apr 07, 2022)
18-46072172-A-T		not specified	Uncertain significance (Apr 25, 2022)

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