PDIA3

protein disulfide isomerase family A member 3, the group of Protein disulfide isomerases

Basic information

Region (hg38): 15:43746394-43773279

Previous symbols: [ "GRP58" ]

Links

ENSG00000167004 ∙ NCBI:2923 ∙ OMIM:602046 ∙ HGNC:4606 ∙ Uniprot:P30101 ∙ 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 PDIA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDIA3 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				2	4	6
missense			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			1		9	10
Total	0	0	21	3	14

Variants in PDIA3

This is a list of pathogenic ClinVar variants found in the PDIA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43746544-G-A		not specified	Uncertain significance (May 17, 2023)
15-43746549-C-T		not specified	Uncertain significance (Feb 10, 2022)
15-43746571-G-T		not specified	Uncertain significance (Nov 30, 2022)
15-43746588-G-T		not specified	Uncertain significance (Nov 21, 2022)
15-43746595-C-T			Benign (Jul 31, 2018)
15-43746616-A-C		not specified	Uncertain significance (Mar 19, 2024)
15-43746618-G-A		not specified	Uncertain significance (Apr 25, 2023)
15-43746645-G-A		not specified	Uncertain significance (Feb 02, 2022)
15-43746701-C-T			Benign (Jun 09, 2021)
15-43753815-C-T		PDIA3-related disorder	Benign (Oct 01, 2018)
15-43753826-G-A		Intellectual disability	Conflicting classifications of pathogenicity (Sep 13, 2024)
15-43753843-C-T		not specified	Uncertain significance (Jun 17, 2024)
15-43756668-C-T		not specified	Uncertain significance (Feb 28, 2024)
15-43756709-C-G		not specified	Uncertain significance (Nov 07, 2023)
15-43761419-C-T		PDIA3-related disorder	Benign (Jun 09, 2021)
15-43761432-G-A		not specified	Uncertain significance (Apr 26, 2024)
15-43761436-G-A		not specified	Uncertain significance (Dec 16, 2021)
15-43761439-A-T		not specified	Uncertain significance (Mar 19, 2024)
15-43761538-A-G		PDIA3-related disorder	Likely benign (Feb 22, 2019)
15-43761689-A-G			Benign (Jun 19, 2021)
15-43763098-G-A		not specified	Uncertain significance (Mar 20, 2024)
15-43763172-G-A		not specified	Likely benign (May 23, 2023)
15-43765434-C-CTT		PDIA3-related disorder	Likely benign (Aug 20, 2019)
15-43765472-T-G		not specified	Uncertain significance (Oct 12, 2021)
15-43765476-A-G		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDIA3	protein_coding	protein_coding	ENST00000300289	13	26888

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00392	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.684	245	277	0.884	0.0000133	3356
Missense in Polyphen		45	95.171	0.47283		1167
Synonymous	0.264	97	100	0.966	0.00000490	917
Loss of Function	4.28	2	25.2	0.0794	0.00000124	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Antigen processing and presentation - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Prion disease pathway;Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Class I MHC mediated antigen processing & presentation;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;Antigen Presentation: Folding, assembly and peptide loading of class I MHC (Consensus)

Recessive Scores

• pRec: 0.444

Intolerance Scores

• loftool: 0.514
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.411
• hipred: Y
• hipred_score: 0.825
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdia3
• Phenotype: cellular phenotype; growth/size/body region phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; hematopoietic system 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: antigen processing and presentation of peptide antigen via MHC class I;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;protein folding;proteolysis;protein folding in endoplasmic reticulum;response to endoplasmic reticulum stress;cell redox homeostasis;oxidation-reduction process;cellular response to interleukin-7;positive regulation of extrinsic apoptotic signaling pathway
• Cellular component: extracellular space;nucleus;endoplasmic reticulum;endoplasmic reticulum lumen;focal adhesion;cell surface;melanosome;MHC class I peptide loading complex;myelin sheath;phagocytic vesicle;recycling endosome membrane;extracellular exosome
• Molecular function: RNA binding;protein disulfide isomerase activity;cysteine-type endopeptidase activity;phospholipase C activity;protein binding;disulfide oxidoreductase activity;peptide disulfide oxidoreductase activity;identical protein binding