PPIL3

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

Basic information

Region (hg38): 2:200870906-200889303

Links

ENSG00000240344 ∙ NCBI:53938 ∙ OMIM:615811 ∙ HGNC:9262 ∙ Uniprot:Q9H2H8 ∙ 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 PPIL3 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIL3 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in PPIL3

This is a list of pathogenic ClinVar variants found in the PPIL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-200871421-T-C		not specified	Uncertain significance (Apr 18, 2023)
2-200871427-T-C		not specified	Uncertain significance (Oct 20, 2021)
2-200871442-C-T		not specified	Uncertain significance (Sep 25, 2023)
2-200871501-G-A		not specified	Uncertain significance (Mar 29, 2023)
2-200881452-T-C		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPIL3	protein_coding	protein_coding	ENST00000286175	6	18397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.902	0.0968	124128	0	3	124131	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.149	66	69.5	0.950	0.00000319	1080
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000336	0.0000336
Other	0.00	0.00

dbNSFP

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.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0933

Intolerance Scores

• loftool: 0.595
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.103
• hipred: Y
• hipred_score: 0.615
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.473

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppil3
• Phenotype: skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome;protein peptidyl-prolyl isomerization;protein folding
• Cellular component: catalytic step 2 spliceosome
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;protein binding