PFN3
Basic information
Region (hg38): 5:177400109-177400661
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PFN3 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 | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 0 |
Variants in PFN3
This is a list of pathogenic ClinVar variants found in the PFN3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-177400168-C-T | not specified | Likely benign (May 06, 2024) | ||
| 5-177400177-T-A | not specified | Uncertain significance (Sep 30, 2024) | ||
| 5-177400186-C-G | not specified | Uncertain significance (Jan 17, 2024) | ||
| 5-177400285-C-T | not specified | Uncertain significance (Sep 03, 2024) | ||
| 5-177400299-A-G | not specified | Uncertain significance (Dec 17, 2023) | ||
| 5-177400329-T-A | not specified | Uncertain significance (Jul 10, 2024) | ||
| 5-177400351-C-G | not specified | Uncertain significance (Aug 14, 2024) | ||
| 5-177400389-C-A | not specified | Uncertain significance (Nov 09, 2021) | ||
| 5-177400416-G-A | not specified | Uncertain significance (Mar 02, 2023) | ||
| 5-177400422-G-A | not specified | Uncertain significance (Jan 11, 2023) | ||
| 5-177400537-C-G | not specified | Uncertain significance (Jan 08, 2025) | ||
| 5-177400537-C-T | not specified | Uncertain significance (Jul 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PFN3 | protein_coding | protein_coding | ENST00000358571 | 1 | 530 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.501 | 0.432 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.480 | 85 | 98.4 | 0.864 | 0.00000720 | 849 |
| Missense in Polyphen | 36 | 36.726 | 0.98023 | 366 | ||
| Synonymous | 0.245 | 45 | 47.1 | 0.955 | 0.00000376 | 318 |
| Loss of Function | 1.29 | 0 | 1.95 | 0.00 | 8.48e-8 | 18 |
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 | 0.00 | 0.00 |
| 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:
- Function
- FUNCTION: Binds to actin and affects the structure of the cytoskeleton. Slightly reduces actin polymerization. Binds to poly-L-proline, phosphatidylinositol 3-phosphate (PtdIns(3)P), phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) and phosphatidylinositol 4-phosphate (PtdIns(4)P). May be involved in spermatogenesis. {ECO:0000269|PubMed:19419568}.;
- 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
(Consensus)
Haploinsufficiency Scores
- pHI
- 0.113
- hipred
- N
- hipred_score
- 0.449
- ghis
- 0.479
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pfn3
- Phenotype
Gene ontology
- Biological process
- actin cytoskeleton organization;regulation of actin filament polymerization;positive regulation of actin filament bundle assembly
- Cellular component
- nucleus;cytoplasm;cytoskeleton
- Molecular function
- actin binding;lipid binding