PPIC

protein-coding

peptidylprolyl isomerase C, the group of Cyclophilin peptidylprolyl isomerases

Gene summary

The protein encoded by this gene is a member of the peptidyl-prolyl cis-trans isomerase (PPIase)) family. PPIases catalyze the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and accelerate the folding of proteins. Similar to other PPIases, this protein can bind immunosuppressant cyclosporin A. [provided by RefSeq, Jul 2008]

MANE transcript

NM_000943.5

Inheritance

—

ClinVar variants

U:34B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr5:123,023,250-123,036,725

External References & Databases

Ensembl (ENSG00000168938)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPIC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000943.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			30 clinvar	1 clinvar		31
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	34	2	0	36

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000943.5	RefSeq	NP_000934.1	5	MANE Select
ENST00000306442.5	Ensembl	ENSP00000303057.4	5	MANE Select
ENST00000910735.1	Ensembl	ENSP00000580794.1	5	Standard
ENST00000910735.2	Ensembl	ENSP00000580794.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein peptidyl-prolyl isomerization
protein folding
protein refolding

Molecular Function

peptidyl-prolyl cis-trans isomerase activity
protein binding
cyclosporin A binding
unfolded protein binding

Cellular Component

cytoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306442
Coding exons: 5
Length: 13492
Individuals with no LoFs: 124478
Homozygous LoFs: 7
Heterozygous LoFs: 1262
Defined: 125747
p: 0.00506

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0754	118	120	0.981	0.00000596	1377
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.0046	0.0045	notable
Ashkenazi Jewish	0.014	0.013	notable
East Asian	0.00011	0.00011	rare
Finnish	0.00074	0.00074	rare
European (Non-Finnish)	0.0075	0.0074	notable
South Asian	0.0019	0.0018	notable
Other	0.0086	0.0083	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0482

Gene Damage Prediction

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