PPIL3

protein-coding

peptidylprolyl isomerase like 3, the group of Cyclophilin peptidylprolyl isomerases|Spliceosomal C complex|Spliceosomal P complex

Gene summary

This gene encodes a member of the cyclophilin family. Cyclophilins catalyze the cis-trans isomerization of peptidylprolyl imide bonds in oligopeptides. They have been proposed to act either as catalysts or as molecular chaperones in protein-folding events. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2008]

MANE transcript

NM_130906.3

Inheritance

—

ClinVar variants

U:19B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr2:200,870,907-200,889,303

External References & Databases

Ensembl (ENSG00000240344)

Transcript & Mutation Effects

hg38 • Region Span ~18.4 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 PPIL3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 17

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_130906.3. 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			1 clinvar			1
missense			16 clinvar	1 clinvar		17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	19	1	0	20

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 107 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_130906.3	RefSeq	NP_570981.1	6	MANE Select
ENST00000392283.9	Ensembl	ENSP00000376107.4	6	MANE Select
NM_032472.4	RefSeq	NP_115861.1	6	Standard
ENST00000286175.12	Ensembl	ENSP00000286175.8	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

mRNA splicing, via spliceosome
protein peptidyl-prolyl isomerization
protein folding

Molecular Function

peptidyl-prolyl cis-trans isomerase activity
protein binding

Cellular Component

catalytic step 2 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000286175
Coding exons: 6
Length: 18397
Individuals with no LoFs: 124128
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 124131
p: 0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.149	66	69.5	0.950	0.00000319	1080
Missense (PolyPhen)		19	23.529	0.80752		316
Synonymous	-0.309	27	25.0	1.08	0.00000123	303
Loss of Function	2.54	0	7.52	0.00	4.03e-7	119

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000034	0.000034	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. May be involved in pre-mRNA splicing.;

Recessive Scores

pRec: 0.0933

Intolerance Scores

LoFtool: 0.595
RVIS EVS: 0.28
RVIS percentile EVS: 71.08

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.473

Gene Damage Prediction

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