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.

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.

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					1	1
missense			48	3		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	3	1

Variants in PDIA4

This is a list of pathogenic ClinVar variants found in the PDIA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-149003868-T-C		not specified	Uncertain significance (Mar 28, 2024)
7-149003900-T-G		not specified	Uncertain significance (Nov 03, 2023)
7-149003904-C-T		not specified	Uncertain significance (Sep 01, 2021)
7-149003916-C-T		not specified	Uncertain significance (Mar 31, 2024)
7-149003948-T-C		not specified	Uncertain significance (Feb 06, 2025)
7-149003955-C-A		not specified	Uncertain significance (Sep 16, 2021)
7-149003963-A-T		not specified	Uncertain significance (Oct 29, 2021)
7-149003979-C-T		not specified	Uncertain significance (Mar 07, 2023)
7-149003991-C-T		not specified	Uncertain significance (Dec 20, 2023)
7-149004012-C-T		not specified	Uncertain significance (Aug 20, 2024)
7-149004035-T-C		not specified	Likely benign (May 22, 2023)
7-149004042-C-T		not specified	Uncertain significance (Dec 06, 2021)
7-149004075-G-A		not specified	Uncertain significance (Feb 12, 2025)
7-149004096-C-T		not specified	Uncertain significance (Oct 06, 2022)
7-149004120-T-C		not specified	Uncertain significance (May 18, 2023)
7-149004137-C-T		not specified	Uncertain significance (Jun 22, 2021)
7-149004149-T-C		not specified	Uncertain significance (Jan 23, 2024)
7-149004159-C-T		not specified	Uncertain significance (Nov 15, 2024)
7-149004164-T-C		not specified	Uncertain significance (Dec 04, 2024)
7-149005165-C-T		not specified	Uncertain significance (Oct 27, 2022)
7-149005188-T-C		not specified	Uncertain significance (Feb 03, 2022)
7-149005209-T-C		not specified	Uncertain significance (Nov 25, 2024)
7-149005264-G-A		not specified	Uncertain significance (May 24, 2023)
7-149005326-G-T		not specified	Uncertain significance (Oct 12, 2024)
7-149005357-T-G		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDIA4	protein_coding	protein_coding	ENST00000286091	10	25580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0780	0.922	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.126	367	360	1.02	0.0000198	4256
Missense in Polyphen		116	135	0.85927		1584
Synonymous	-0.743	167	155	1.08	0.0000104	1206
Loss of Function	3.43	7	25.8	0.271	0.00000119	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.000218	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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

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

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