PPID

peptidylprolyl isomerase D, the group of Cyclophilin peptidylprolyl isomerases|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 4:158709127-158723396

Links

ENSG00000171497 ∙ NCBI:5481 ∙ OMIM:601753 ∙ HGNC:9257 ∙ Uniprot:Q08752 ∙ 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 PPID gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPID 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			14	1	1	16
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	14	2	2

Variants in PPID

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

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

Position	Type	Phenotype	Significance	ClinVar
4-158709746-A-G		not specified	Uncertain significance (May 30, 2024)
4-158709772-A-G			Likely benign (Aug 01, 2024)
4-158710644-T-C		not specified	Uncertain significance (Sep 27, 2021)
4-158710646-T-C		not specified	Uncertain significance (Jun 03, 2024)
4-158710767-C-T		not specified	Uncertain significance (Feb 06, 2024)
4-158710808-C-T		not specified	Uncertain significance (Mar 29, 2022)
4-158710848-C-G		not specified	Uncertain significance (Apr 06, 2024)
4-158713151-T-C		not specified	Likely benign (Feb 27, 2023)
4-158713201-A-G		not specified	Uncertain significance (Jun 28, 2023)
4-158713237-A-G		not specified	Uncertain significance (Jan 04, 2024)
4-158713256-C-T		not specified	Uncertain significance (Jul 30, 2023)
4-158715390-A-G		not specified	Uncertain significance (Mar 30, 2024)
4-158715394-T-G		not specified	Uncertain significance (Jun 13, 2024)
4-158715602-T-G		not specified	Uncertain significance (Sep 12, 2023)
4-158715633-T-C		not specified	Uncertain significance (Mar 15, 2024)
4-158715666-A-C		not specified	Uncertain significance (Apr 22, 2024)
4-158715678-C-T			Benign (Apr 10, 2018)
4-158717095-CAT-C			Likely benign (Aug 23, 2018)
4-158717121-G-C		not specified	Uncertain significance (Jun 19, 2024)
4-158717149-C-T		not specified	Uncertain significance (May 24, 2024)
4-158719171-C-G			Benign (Jun 18, 2018)
4-158719235-G-A		not specified	Uncertain significance (Mar 15, 2024)
4-158719251-A-G		not specified	Uncertain significance (Dec 01, 2022)
4-158721387-G-A		not specified	Uncertain significance (May 09, 2023)
4-158721414-C-A		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPID	protein_coding	protein_coding	ENST00000307720	10	14263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.93e-9	0.417	125251	0	496	125747	0.00197

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.606	171	195	0.878	0.00000967	2431
Missense in Polyphen		68	73.514	0.925		951
Synonymous	-1.37	83	68.5	1.21	0.00000375	663
Loss of Function	0.973	16	20.8	0.770	0.00000101	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00287	0.00287
Ashkenazi Jewish	0.00456	0.00457
East Asian	0.00870	0.00874
Finnish	0.00116	0.00116
European (Non-Finnish)	0.00121	0.00120
Middle Eastern	0.00870	0.00874
South Asian	0.00147	0.00147
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:11350175, PubMed:20676357). Proposed to act as a co-chaperone in HSP90 complexes such as in unligated steroid receptors heterocomplexes. Different co- chaperones seem to compete for association with HSP90 thus establishing distinct HSP90-co-chaperone-receptor complexes with the potential to exert tissue-specific receptor activity control. May have a preference for estrogen receptor complexes and is not found in glucocorticoid receptor complexes. May be involved in cytoplasmic dynein-dependent movement of the receptor from the cytoplasm to the nucleus. May regulate MYB by inhibiting its DNA- binding activity. Involved in regulation of AHR signaling by promoting the formation of the AHR:ARNT dimer; the function is independent of HSP90 but requires the chaperone activity. Involved in regulation of UV radiation-induced apoptosis. Promotes cell viability in anaplastic lymphoma kinase-positive anaplastic large- cell lymphoma (ALK+ ALCL) cell lines. {ECO:0000269|PubMed:11350175, ECO:0000269|PubMed:18708059, ECO:0000269|PubMed:20676357, ECO:0000269|PubMed:22681779, ECO:0000269|PubMed:23220213, ECO:0000269|PubMed:9659917}.
• Pathway: Necroptosis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);NO-cGMP-PKG mediated Neuroprotection;Signal Transduction;Signaling by Nuclear Receptors;C-MYB transcription factor network;ESR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.880
• rvis_EVS: 0.77
• rvis_percentile_EVS: 87.01

Haploinsufficiency Scores

• pHI: 0.245
• hipred: N
• hipred_score: 0.454
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppid

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;protein peptidyl-prolyl isomerization;protein folding;apoptotic process;protein transport;viral release from host cell;lipid droplet organization;protein refolding;positive regulation of apoptotic process;positive regulation of viral genome replication;positive regulation of protein secretion;chaperone-mediated protein folding;protein-containing complex assembly;cellular response to UV-A
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;protein binding;transcription factor binding;cyclosporin A binding;estrogen receptor binding;Hsp70 protein binding;heat shock protein binding;unfolded protein binding;Hsp90 protein binding