PPIC

peptidylprolyl isomerase C, the group of Cyclophilin peptidylprolyl isomerases

Basic information

Region (hg38): 5:123023249-123036725

Links

ENSG00000168938 ∙ NCBI:5480 ∙ OMIM:123842 ∙ HGNC:9256 ∙ Uniprot:P45877 ∙ 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 PPIC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIC 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			9	1		10
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in PPIC

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

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

Position	Type	Phenotype	Significance	ClinVar
5-123023880-A-C		not specified	Uncertain significance (Dec 14, 2023)
5-123023886-C-T		not specified	Uncertain significance (Oct 03, 2022)
5-123023946-T-C		not specified	Likely benign (Jul 14, 2021)
5-123023959-G-T		not specified	Uncertain significance (Dec 20, 2021)
5-123025905-C-T		not specified	Uncertain significance (Oct 27, 2022)
5-123025924-G-C		not specified	Uncertain significance (Jan 19, 2024)
5-123028777-C-T		not specified	Uncertain significance (May 24, 2024)
5-123029312-G-A		not specified	Uncertain significance (Apr 07, 2023)
5-123029340-T-C		not specified	Uncertain significance (Jan 23, 2023)
5-123029387-TC-T			Likely benign (Mar 01, 2023)
5-123036526-G-T		not specified	Uncertain significance (Jun 04, 2024)
5-123036559-A-G		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPIC	protein_coding	protein_coding	ENST00000306442	5	13492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000305	0.592	124478	7	1262	125747	0.00506

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0754	118	120	0.981	0.00000596	1377
Missense in Polyphen		55	54.031	1.0179		651
Synonymous	0.157	45	46.4	0.971	0.00000243	432
Loss of Function	0.587	6	7.76	0.773	3.26e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00558	0.00557
Ashkenazi Jewish	0.0135	0.0133
East Asian	0.000109	0.000109
Finnish	0.000742	0.000739
European (Non-Finnish)	0.00748	0.00740
Middle Eastern	0.000109	0.000109
South Asian	0.00191	0.00183
Other	0.00860	0.00834

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. {ECO:0000269|PubMed:20676357}.

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.797
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.4

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.251
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0482

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppic

Gene ontology

• Biological process: protein peptidyl-prolyl isomerization;protein folding;protein refolding
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;protein binding;cyclosporin A binding;unfolded protein binding