GeneBe

PDIA4

protein disulfide isomerase family A member 4, the group of Protein disulfide isomerases

Basic information

Region (hg38): 7:149003062-149028662

Links

ENSG00000155660 ∙ NCBI:9601 ∙ OMIM:620018 ∙ HGNC:30167 ∙ Uniprot:P13667 ∙ 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 PDIA4 gene.

  • not_specified (82 variants)
  • not_provided (2 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDIA4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004911.5. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
78
clinvar
6
clinvar
 84
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 78 6 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PDIA4protein_codingprotein_codingENST00000286091 1025580
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.07800.9221257320161257480.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1263673601.020.00001984256
Missense in Polyphen1161350.859271584
Synonymous-0.7431671551.080.00001041206
Loss of Function3.43725.80.2710.00000119341

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.000.00
European (Non-Finnish)0.00008870.0000879
Middle Eastern0.0002180.000217
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Pathway
Thyroid hormone synthesis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Ibuprofen Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Ibuprofen Metabolism Pathway;Morphine Metabolism Pathway;Irinotecan Action Pathway;Morphine Action Pathway;Etoposide Action Pathway;Sorafenib Metabolism Pathway;Acetaminophen Metabolism Pathway;Vitamin A Deficiency;Irinotecan Metabolism Pathway;Etoposide Metabolism Pathway;Retinol Metabolism (Consensus)

Intolerance Scores

loftool
0.522
rvis_EVS
-0.19
rvis_percentile_EVS
39.25

Haploinsufficiency Scores

pHI
0.227
hipred
Y
hipred_score
0.694
ghis
0.493

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.859

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pdia4
Phenotype
hematopoietic system phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
protein folding;protein secretion;response to endoplasmic reticulum stress;cell redox homeostasis;oxidation-reduction process;chaperone-mediated protein folding
Cellular component
extracellular space;endoplasmic reticulum;endoplasmic reticulum lumen;cell surface;melanosome
Molecular function
RNA binding;protein disulfide isomerase activity;protein binding;peptide disulfide oxidoreductase activity