PFDN2
Basic information
Region (hg38): 1:161100555-161118055
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 PFDN2 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in PFDN2
This is a list of pathogenic ClinVar variants found in the PFDN2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-161100735-T-C | not specified | Uncertain significance (Oct 07, 2022) | ||
| 1-161102085-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
| 1-161117956-T-G | not specified | Uncertain significance (Nov 13, 2023) | ||
| 1-161117977-C-T | not specified | Uncertain significance (Jun 11, 2024) | ||
| 1-161118002-C-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 1-161118007-C-T | not specified | Uncertain significance (Apr 12, 2024) | ||
| 1-161118011-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 1-161118018-C-A | not specified | Uncertain significance (Sep 26, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PFDN2 | protein_coding | protein_coding | ENST00000368010 | 4 | 17556 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.350 | 0.638 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.500 | 80 | 93.6 | 0.855 | 0.00000533 | 993 |
| Missense in Polyphen | 17 | 28.202 | 0.60279 | 297 | ||
| Synonymous | -0.647 | 39 | 34.2 | 1.14 | 0.00000168 | 308 |
| Loss of Function | 2.12 | 2 | 8.76 | 0.228 | 5.40e-7 | 92 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000934 | 0.0000924 |
| 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 specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins. {ECO:0000269|PubMed:9630229}.;
- Pathway
- Metabolism of proteins;Chaperonin-mediated protein folding;Protein folding;Prefoldin mediated transfer of substrate to CCT/TriC;TNFalpha;Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.316
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.712
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pfdn2
- Phenotype
- 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);
Gene ontology
- Biological process
- protein folding;positive regulation of cytoskeleton organization
- Cellular component
- nucleus;cytoplasm;mitochondrion;cytosol;prefoldin complex
- Molecular function
- protein binding;protein folding chaperone;unfolded protein binding