PDIA2

protein disulfide isomerase family A member 2, the group of Protein disulfide isomerases

Basic information

Region (hg38): 16:283164-287215

Previous symbols: [ "PDIP" ]

Links

ENSG00000185615 ∙ NCBI:64714 ∙ OMIM:608012 ∙ HGNC:14180 ∙ Uniprot:Q13087 ∙ 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 PDIA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDIA2 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				5	2	7
missense			70	5		75
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	11	2

Variants in PDIA2

This is a list of pathogenic ClinVar variants found in the PDIA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-283176-C-T		not specified	Uncertain significance (Nov 20, 2024)
16-283220-G-A			Likely benign (Sep 01, 2022)
16-283270-C-T		not specified	Uncertain significance (Dec 07, 2024)
16-283315-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-283321-C-G		not specified	Uncertain significance (Sep 14, 2022)
16-283351-C-T		not specified	Uncertain significance (Feb 13, 2024)
16-284399-G-A		not specified	Uncertain significance (Sep 29, 2022)
16-284446-G-A		not specified	Uncertain significance (Jun 17, 2024)
16-284452-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-284453-C-T		not specified	Uncertain significance (Jun 23, 2023)
16-284503-C-T		not specified	Uncertain significance (Jul 13, 2021)
16-284505-C-T			Likely benign (Jul 01, 2024)
16-284506-G-A		not specified	Uncertain significance (Dec 17, 2023)
16-284539-C-G		not specified	Uncertain significance (Aug 14, 2024)
16-284557-C-T		not specified	Uncertain significance (Sep 30, 2024)
16-284558-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-284570-G-A			Uncertain significance (May 31, 2019)
16-284573-C-T		not specified	Uncertain significance (Jun 22, 2024)
16-284575-C-T		not specified	Uncertain significance (Dec 21, 2021)
16-284579-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-284581-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-284584-G-A		not specified	Uncertain significance (Jun 02, 2024)
16-284590-A-G		not specified	Uncertain significance (Oct 05, 2021)
16-284662-C-T		not specified	Uncertain significance (May 09, 2023)
16-284670-G-A		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDIA2	protein_coding	protein_coding	ENST00000219406	11	4064

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.45e-33	3.16e-8	119718	40	5017	124775	0.0205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.73	418	330	1.27	0.0000224	3347
Missense in Polyphen		134	108.09	1.2397		1264
Synonymous	-5.42	237	152	1.56	0.0000115	1103
Loss of Function	-3.30	39	22.2	1.75	0.00000102	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0575	0.0527
Ashkenazi Jewish	0.0604	0.0397
East Asian	0.000841	0.000668
Finnish	0.0294	0.0263
European (Non-Finnish)	0.0278	0.0198
Middle Eastern	0.000841	0.000668
South Asian	0.0325	0.0235
Other	0.0333	0.0249

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an intracellular estrogen-binding protein. May be involved in modulating cellular levels and biological functions of estrogens in the pancreas. May act as a chaperone that inhibits aggregation of misfolded proteins. {ECO:0000269|PubMed:19150607, ECO:0000269|PubMed:19429457}.
• Pathway: 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;Demo complete;Statin Pathway;Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.974
• rvis_EVS: 2.7
• rvis_percentile_EVS: 98.9

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.318
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdia2

Gene ontology

• Biological process: protein folding;protein retention in ER lumen;peptidyl-proline hydroxylation;protein folding in endoplasmic reticulum;response to endoplasmic reticulum stress;cell redox homeostasis;oxidation-reduction process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: steroid binding;protein binding;disulfide oxidoreductase activity;peptide disulfide oxidoreductase activity