PPIE

Basic information

Region (hg38): 1:39692182-39763914

Links

ENSG00000084072

∙ NCBI:10450 ∙ OMIM:602435 ∙ HGNC:9258 ∙ Uniprot:Q9UNP9 ∙ 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 PPIE gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIE 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			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			9 clinvar	4 clinvar	1 clinvar	14
Total	0	0	24	4	1

Variants in PPIE

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

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

Position	Phenotype	Significance	ClinVar
1-39741368-A-G	not specified	Uncertain significance (May 25, 2022)	2406552
1-39741389-G-A	not specified	Uncertain significance (Feb 23, 2023)	2458408
1-39743243-A-G	not specified	Uncertain significance (Jun 07, 2024)	3309183
1-39743247-G-A	not specified	Uncertain significance (Jan 03, 2024)	3217192
1-39743922-G-A	not specified	Uncertain significance (Apr 29, 2024)	3309184
1-39745399-C-T	not specified	Uncertain significance (Jul 06, 2021)	2235180
1-39745445-C-T	not specified	Uncertain significance (Jul 29, 2023)	2593778
1-39748912-G-A	not specified	Uncertain significance (Apr 22, 2022)	2284751
1-39748932-A-G	not specified	Uncertain significance (Dec 01, 2022)	2331029
1-39748940-T-G	not specified	Uncertain significance (Sep 22, 2023)	3217193
1-39748945-T-G	not specified	Uncertain significance (Nov 10, 2022)	2325553
1-39748983-A-G	not specified	Uncertain significance (Aug 02, 2023)	2596636
1-39748990-A-G	not specified	Uncertain significance (Dec 15, 2023)	3217194
1-39749014-A-G	not specified	Uncertain significance (Oct 25, 2022)	2388516
1-39752951-T-A	not specified	Uncertain significance (Mar 01, 2023)	2492516
1-39752970-G-A	not specified	Uncertain significance (Sep 16, 2021)	2250832
1-39753041-C-T	not specified	Uncertain significance (Dec 08, 2023)	3217195
1-39760430-C-T	not specified	Uncertain significance (Oct 12, 2021)	2359152
1-39760448-T-G	not specified	Uncertain significance (Sep 26, 2023)	3134578
1-39760453-C-A	not specified	Uncertain significance (Sep 13, 2023)	2603342
1-39760533-C-T		Likely benign (Dec 01, 2022)	2638715
1-39760534-G-A	not specified	Uncertain significance (Jul 13, 2021)	2216896
1-39760553-G-T	not specified	Uncertain significance (Feb 27, 2023)	2490046
1-39762513-T-C		Benign/Likely benign (Sep 01, 2023)	773107
1-39763082-T-C		Benign (May 03, 2018)	780000

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPIE	protein_coding	protein_coding	ENST00000372830	10	71733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.728	0.272	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	133	180	0.737	0.00000999	2088
Missense in Polyphen		56	100.34	0.55809		1155
Synonymous	0.234	62	64.4	0.963	0.00000360	568
Loss of Function	3.20	3	17.4	0.172	8.22e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28076346). Combines RNA- binding and PPIase activities (PubMed:8977107, PubMed:18258190, PubMed:20677832, PubMed:20460131). Binds mRNA and has a preference for single-stranded RNA molecules with poly-A and poly-U stretches, suggesting it binds to the poly(A)-region in the 3'-UTR of mRNA molecules (PubMed:8977107, PubMed:18258190, PubMed:20460131). Catalyzes the cis-trans isomerization of proline imidic peptide bonds in proteins (PubMed:8977107, PubMed:18258190, PubMed:20677832, PubMed:20541251). Inhibits KMT2A activity; this requires proline isomerase activity (PubMed:20677832, PubMed:20541251, PubMed:20460131). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:18258190, ECO:0000269|PubMed:20460131, ECO:0000269|PubMed:20541251, ECO:0000269|PubMed:20677832, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:8977107}.;
Pathway: Spliceosome - Homo sapiens (human);DNA Repair;Neutrophil degranulation;Metabolism of RNA;Innate Immune System;Immune System;mRNA Splicing - Major Pathway;Formation of TC-NER Pre-Incision Complex;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

pRec: 0.110

Intolerance Scores

loftool: 0.284
rvis_EVS: -0.43
rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

pHI: 0.235
hipred: Y
hipred_score: 0.665
ghis: 0.622

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ppie
Phenotype

Gene ontology

Biological process: mRNA splicing, via spliceosome;protein peptidyl-prolyl isomerization;transcription-coupled nucleotide-excision repair;regulation of transcription, DNA-templated;protein folding;protein refolding;neutrophil degranulation;positive regulation of viral genome replication
Cellular component: extracellular region;nucleus;nucleoplasm;cytosol;nuclear speck;secretory granule lumen;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;ficolin-1-rich granule lumen
Molecular function: RNA binding;mRNA binding;peptidyl-prolyl cis-trans isomerase activity;protein binding;poly(A) binding;cyclosporin A binding;unfolded protein binding