PPIL2

peptidylprolyl isomerase like 2, the group of Spliceosomal Bact complex|Cyclophilin peptidylprolyl isomerases|U-box domain containing

Basic information

Region (hg38): 22:21666000-21700015

Links

ENSG00000100023 ∙ NCBI:23759 ∙ OMIM:607588 ∙ HGNC:9261 ∙ Uniprot:Q13356 ∙ 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 PPIL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIL2 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					1	1
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	1

Variants in PPIL2

This is a list of pathogenic ClinVar variants found in the PPIL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-21666113-A-G		not specified	Uncertain significance (Nov 09, 2023)
22-21671020-A-C		not specified	Uncertain significance (Oct 25, 2023)
22-21671037-G-A		not specified	Uncertain significance (Jun 21, 2023)
22-21672356-A-G		not specified	Uncertain significance (Jun 17, 2022)
22-21675109-A-G		not specified	Uncertain significance (Feb 23, 2023)
22-21681335-C-A		not specified	Uncertain significance (Jun 22, 2024)
22-21681335-C-G		not specified	Uncertain significance (Aug 26, 2022)
22-21681375-C-T			Benign (Mar 29, 2018)
22-21681382-G-A		not specified	Uncertain significance (Apr 26, 2023)
22-21682490-C-G		not specified	Uncertain significance (Jun 05, 2024)
22-21682503-C-T		not specified	Uncertain significance (Dec 20, 2023)
22-21683186-C-T		not specified	Uncertain significance (May 03, 2023)
22-21683215-A-G		not specified	Uncertain significance (Dec 08, 2021)
22-21683254-C-T		not specified	Uncertain significance (Jun 11, 2024)
22-21684773-G-A		not specified	Uncertain significance (Jan 08, 2024)
22-21684797-A-G		not specified	Uncertain significance (May 04, 2023)
22-21684848-G-C		not specified	Uncertain significance (Feb 15, 2023)
22-21686486-C-A		not specified	Uncertain significance (May 18, 2023)
22-21686529-C-T		not specified	Uncertain significance (Jan 04, 2022)
22-21686547-C-T		not specified	Uncertain significance (Dec 30, 2023)
22-21686916-G-A		not specified	Uncertain significance (Jun 11, 2021)
22-21686963-A-G		not specified	Uncertain significance (Oct 06, 2021)
22-21687694-G-A		not specified	Uncertain significance (Mar 11, 2024)
22-21687721-C-T		not specified	Uncertain significance (Jan 26, 2022)
22-21687722-G-A		not specified	Uncertain significance (Nov 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPIL2	protein_coding	protein_coding	ENST00000412327	21	47746

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000823	0.999	125666	1	81	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	247	331	0.746	0.0000204	3487
Missense in Polyphen		61	106.45	0.57304		1136
Synonymous	0.171	130	133	0.981	0.00000908	960
Loss of Function	3.65	12	35.5	0.338	0.00000169	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.00126	0.00121
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a ubiquitin-protein ligase activity acting as an E3 ubiquitin protein ligase or as an ubiquitin-ubiquitin ligase promoting elongation of ubiquitin chains on substrates. By mediating 'Lys-48'-linked polyubiquitination of proteins could target them for proteasomal degradation (PubMed:11435423). May also function as a chaperone, playing a role in transport to the cell membrane of BSG/Basigin for instance (PubMed:15946952). Probable inactive PPIase with no peptidyl-prolyl cis-trans isomerase activity (PubMed:20676357). {ECO:0000269|PubMed:11435423, ECO:0000269|PubMed:15946952, ECO:0000269|PubMed:20676357}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.875
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.19

Haploinsufficiency Scores

• pHI: 0.241
• hipred: Y
• hipred_score: 0.625
• ghis: 0.622

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppil2

Gene ontology

• Biological process: protein polyubiquitination;protein peptidyl-prolyl isomerization;protein folding;leukocyte migration;protein localization to plasma membrane
• Cellular component: nucleus;nucleoplasm;cytoplasm;Golgi lumen;plasma membrane
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;protein binding;cyclosporin A binding;ubiquitin-ubiquitin ligase activity;ubiquitin protein ligase activity