PDIA5
Basic information
Region (hg38): 3:123067025-123225227
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (76 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDIA5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006810.4. 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 | 0 | |||||
missense | 74 | 76 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 74 | 2 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PDIA5 | protein_coding | protein_coding | ENST00000316218 | 17 | 158166 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.15e-9 | 0.983 | 125676 | 0 | 72 | 125748 | 0.000286 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.238 | 283 | 295 | 0.961 | 0.0000167 | 3428 |
Missense in Polyphen | 92 | 101.41 | 0.90719 | 1201 | ||
Synonymous | -0.422 | 127 | 121 | 1.05 | 0.00000780 | 942 |
Loss of Function | 2.32 | 20 | 34.7 | 0.576 | 0.00000190 | 404 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000981 | 0.000981 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000158 | 0.000158 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000786 | 0.000784 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Pathway
- XBP1(S) activates chaperone genes
(Consensus)
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- loftool
- 0.790
- rvis_EVS
- -0.95
- rvis_percentile_EVS
- 9.21
Haploinsufficiency Scores
- pHI
- 0.237
- hipred
- N
- hipred_score
- 0.492
- ghis
- 0.568
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.580
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pdia5
- Phenotype
Zebrafish Information Network
- Gene name
- pdia5
- Affected structure
- thrombocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein folding;IRE1-mediated unfolded protein response;cell redox homeostasis;oxidation-reduction process
- Cellular component
- endoplasmic reticulum lumen;endoplasmic reticulum membrane
- Molecular function
- protein disulfide isomerase activity;protein binding;peptide disulfide oxidoreductase activity;oxidoreductase activity