PDIA5

protein disulfide isomerase family A member 5, the group of MicroRNA protein coding host genes|Protein disulfide isomerases

Basic information

Region (hg38): 3:123067024-123225227

Links

ENSG00000065485 ∙ NCBI:10954 ∙ OMIM:616942 ∙ HGNC:24811 ∙ Uniprot:Q14554 ∙ 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 PDIA5 gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDIA5 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in PDIA5

This is a list of pathogenic ClinVar variants found in the PDIA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-123089180-T-C		not specified	Uncertain significance (Aug 17, 2022)
3-123089262-G-A		not specified	Uncertain significance (Sep 06, 2022)
3-123092361-C-T		not specified	Uncertain significance (Oct 02, 2023)
3-123092420-A-G		not specified	Uncertain significance (Dec 16, 2022)
3-123102449-T-C		not specified	Uncertain significance (Mar 27, 2023)
3-123102786-T-C		not specified	Uncertain significance (May 11, 2022)
3-123102794-A-G		not specified	Uncertain significance (Oct 29, 2021)
3-123106750-C-A		not specified	Uncertain significance (Dec 08, 2023)
3-123106833-A-G		not specified	Uncertain significance (Aug 13, 2021)
3-123106834-G-T		not specified	Uncertain significance (Sep 26, 2023)
3-123110973-G-T		not specified	Uncertain significance (Dec 27, 2023)
3-123110978-C-T		not specified	Uncertain significance (Jul 12, 2022)
3-123110999-C-T		not specified	Uncertain significance (Dec 03, 2021)
3-123111002-C-G		not specified	Uncertain significance (Feb 05, 2024)
3-123124141-A-G		not specified	Uncertain significance (Jul 12, 2023)
3-123124147-T-A		not specified	Uncertain significance (Sep 17, 2021)
3-123130505-C-T		not specified	Uncertain significance (May 11, 2022)
3-123130532-G-A		not specified	Uncertain significance (Aug 21, 2023)
3-123130553-G-A		not specified	Uncertain significance (Mar 01, 2023)
3-123146117-G-C		not specified	Uncertain significance (Aug 04, 2023)
3-123146120-G-C		not specified	Uncertain significance (Dec 03, 2021)
3-123146257-A-T		not specified	Uncertain significance (Mar 21, 2023)
3-123150248-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-123150253-C-A		not specified	Uncertain significance (Feb 22, 2023)
3-123150350-T-C		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDIA5	protein_coding	protein_coding	ENST00000316218	17	158166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-9	0.983	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.238	283	295	0.961	0.0000167	3428
Missense in Polyphen		92	101.41	0.90719		1201
Synonymous	-0.422	127	121	1.05	0.00000780	942
Loss of Function	2.32	20	34.7	0.576	0.00000190	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000981	0.000981
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000786	0.000784
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: XBP1(S) activates chaperone genes (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.790
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.21

Haploinsufficiency Scores

• pHI: 0.237
• hipred: N
• hipred_score: 0.492
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.580

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdia5

Zebrafish Information Network

• Gene name: pdia5
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein folding;IRE1-mediated unfolded protein response;cell redox homeostasis;oxidation-reduction process
• Cellular component: endoplasmic reticulum lumen;endoplasmic reticulum membrane
• Molecular function: protein disulfide isomerase activity;protein binding;peptide disulfide oxidoreductase activity;oxidoreductase activity