PFN2

profilin 2, the group of Profilins

Basic information

Region (hg38): 3:149964904-150050788

Links

ENSG00000070087

∙ NCBI:5217 ∙ OMIM:176590 ∙ HGNC:8882 ∙ Uniprot:P35080 ∙ 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 PFN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PFN2 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				1 clinvar		1
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1 clinvar	1
Total	0	0	3	1	1

Variants in PFN2

This is a list of pathogenic ClinVar variants found in the PFN2 region.

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

Position	Phenotype	Significance	ClinVar
3-149968383-A-G		Likely benign (Mar 01, 2022)	2654226
3-149968402-C-A	not specified	Uncertain significance (May 30, 2024)	3305913
3-149968445-C-T	not specified	Uncertain significance (Jun 13, 2023)	2511259
3-149968534-A-G	not specified	Uncertain significance (May 29, 2024)	3305912
3-149968568-G-GA		Benign (Jan 17, 2024)	2776129
3-149970739-A-C	not specified	Uncertain significance (Jul 15, 2021)	2238007
3-149970750-G-A	not specified	Uncertain significance (Aug 08, 2023)	2596938

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PFN2	protein_coding	protein_coding	ENST00000239940	3	85885

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.421	0.548	124689	0	1	124690	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	26	73.5	0.354	0.00000393	916
Missense in Polyphen		6	28.802	0.20832		376
Synonymous	0.0811	28	28.6	0.981	0.00000175	258
Loss of Function	1.72	1	5.26	0.190	2.21e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG.;
Pathway: Salmonella infection - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Shigellosis - Homo sapiens (human);Association Between Physico-Chemical Features and Toxicity Associated Pathways;Developmental Biology;Signal Transduction;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Signaling by ROBO receptors;Axon guidance (Consensus)

Recessive Scores

pRec: 0.230

Intolerance Scores

loftool: 0.285
rvis_EVS: 0.04
rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

pHI: 0.635
hipred: Y
hipred_score: 0.856
ghis: 0.653

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.642

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pfn2
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); growth/size/body region phenotype; cellular phenotype;

Gene ontology

Biological process: negative regulation of epithelial cell migration;actin cytoskeleton organization;regulation of actin filament polymerization;negative regulation of actin filament polymerization;positive regulation of actin filament polymerization;positive regulation of actin filament bundle assembly;positive regulation of ATPase activity;positive regulation of peptidyl-serine phosphorylation;protein stabilization;positive regulation of stress fiber assembly;modification of postsynaptic actin cytoskeleton;negative regulation of ruffle assembly;regulation of synaptic vesicle exocytosis
Cellular component: cytoplasm;cytoskeleton;extracellular exosome;Schaffer collateral - CA1 synapse;presynapse;postsynapse;glutamatergic synapse
Molecular function: actin binding;actin monomer binding;protein binding;phosphatidylinositol-4,5-bisphosphate binding;ATPase activity