PDIA6

protein disulfide isomerase family A member 6, the group of Protein disulfide isomerases|Thioredoxin domain containing

Basic information

Region (hg38): 2:10783391-10837977

Previous symbols: [ "TXNDC7" ]

Links

ENSG00000143870 ∙ NCBI:10130 ∙ OMIM:611099 ∙ HGNC:30168 ∙ Uniprot:Q15084 ∙ 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 PDIA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDIA6 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						0
missense			37			37
nonsense						0
start loss						0
frameshift		1	1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	38	0	0

Variants in PDIA6

This is a list of pathogenic ClinVar variants found in the PDIA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-10784319-A-G		not specified	Uncertain significance (Nov 25, 2024)
2-10784959-T-G		not specified	Uncertain significance (Nov 26, 2024)
2-10784969-C-A		not specified	Uncertain significance (Aug 28, 2024)
2-10784969-C-G		not specified	Uncertain significance (Jun 12, 2023)
2-10784969-C-T		not specified	Uncertain significance (Feb 05, 2024)
2-10784990-C-G		not specified	Uncertain significance (Aug 04, 2021)
2-10787317-C-G		not specified	Uncertain significance (Feb 13, 2024)
2-10787347-G-A		not specified	Uncertain significance (May 30, 2024)
2-10787396-C-T		not specified	Uncertain significance (Dec 13, 2021)
2-10787434-A-T		not specified	Uncertain significance (Oct 01, 2024)
2-10788748-T-C		not specified	Uncertain significance (Jun 21, 2023)
2-10788915-G-C		not specified	Uncertain significance (Mar 17, 2023)
2-10788927-C-A		not specified	Uncertain significance (Nov 01, 2021)
2-10788975-T-C		not specified	Uncertain significance (Aug 08, 2023)
2-10788977-A-C		not specified	Uncertain significance (Aug 21, 2023)
2-10789768-G-A		not specified	Uncertain significance (Nov 16, 2022)
2-10789805-C-A		not specified	Uncertain significance (Nov 13, 2024)
2-10789830-G-T		not specified	Uncertain significance (Oct 25, 2024)
2-10789870-A-T		not specified	Uncertain significance (Dec 16, 2023)
2-10789882-C-T		not specified	Uncertain significance (Jan 04, 2024)
2-10789886-TA-T		See cases	Likely pathogenic (Nov 14, 2022)
2-10790721-C-T		not specified	Uncertain significance (Aug 28, 2024)
2-10790786-G-A		not specified	Uncertain significance (Jun 16, 2023)
2-10790799-C-T		not specified	Uncertain significance (Aug 26, 2024)
2-10791817-G-A		not specified	Uncertain significance (Aug 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDIA6	protein_coding	protein_coding	ENST00000272227	13	54587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.249	0.751	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.704	219	250	0.875	0.0000143	2854
Missense in Polyphen		56	73.753	0.75929		909
Synonymous	1.09	84	97.7	0.860	0.00000627	843
Loss of Function	3.53	6	25.1	0.239	0.00000122	299

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000101	0.0000967
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a chaperone that inhibits aggregation of misfolded proteins (PubMed:12204115). Negatively regulates the unfolded protein response (UPR) through binding to UPR sensors such as ERN1, which in turn inactivates ERN1 signaling (PubMed:24508390). May also regulate the UPR via the EIF2AK3 UPR sensor (PubMed:24508390). Plays a role in platelet aggregation and activation by agonists such as convulxin, collagen and thrombin (PubMed:15466936). {ECO:0000269|PubMed:12204115, ECO:0000269|PubMed:15466936, ECO:0000269|PubMed:24508390}.
• Pathway: Protein processing in endoplasmic reticulum - 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;XBP1(S) activates chaperone genes;Photodynamic therapy-induced unfolded protein response;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.752
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.198
• hipred: Y
• hipred_score: 0.756
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.783

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdia6

Gene ontology

• Biological process: protein folding;IRE1-mediated unfolded protein response;post-translational protein modification;cellular protein metabolic process;cell redox homeostasis;oxidation-reduction process
• Cellular component: extracellular space;endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;cytosol;plasma membrane;endoplasmic reticulum chaperone complex;melanosome;extracellular exosome
• Molecular function: protein disulfide isomerase activity;protein binding;peptide disulfide oxidoreductase activity