PPIL4

peptidylprolyl isomerase like 4, the group of Cyclophilin peptidylprolyl isomerases|RNA binding motif containing

Basic information

Region (hg38): 6:149504494-149546043

Links

ENSG00000131013 ∙ NCBI:85313 ∙ OMIM:607609 ∙ HGNC:15702 ∙ Uniprot:Q8WUA2 ∙ 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 PPIL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIL4 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			13			13
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in PPIL4

This is a list of pathogenic ClinVar variants found in the PPIL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149505505-C-T		not specified	Uncertain significance (Mar 15, 2024)
6-149505572-T-C		not specified	Uncertain significance (Feb 16, 2023)
6-149505596-A-T		not specified	Uncertain significance (May 23, 2023)
6-149505643-T-A		not specified	Uncertain significance (Jan 04, 2024)
6-149512160-T-C		not specified	Uncertain significance (Dec 17, 2023)
6-149512229-G-A		not specified	Uncertain significance (Mar 29, 2024)
6-149525202-C-T		not specified	Uncertain significance (Oct 05, 2023)
6-149526716-A-T		not specified	Uncertain significance (Jun 30, 2023)
6-149535635-G-T		not specified	Uncertain significance (Feb 15, 2023)
6-149535648-T-C		not specified	Uncertain significance (May 24, 2023)
6-149535689-G-T		not specified	Uncertain significance (Sep 26, 2022)
6-149541416-G-C		not specified	Uncertain significance (Jan 02, 2024)
6-149541526-T-C		not specified	Uncertain significance (May 18, 2022)
6-149541545-T-C		not specified	Uncertain significance (Jun 16, 2024)
6-149541583-C-G		not specified	Uncertain significance (Sep 06, 2022)
6-149545939-G-T		not specified	Uncertain significance (Mar 21, 2023)
6-149545983-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPIL4	protein_coding	protein_coding	ENST00000253329	13	41306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.69e-9	0.956	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	195	259	0.754	0.0000125	3299
Missense in Polyphen		46	79.54	0.57833		992
Synonymous	0.658	79	86.8	0.910	0.00000435	828
Loss of Function	2.06	19	31.4	0.604	0.00000186	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000578	0.000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000272
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000336	0.000325
Middle Eastern	0.000278	0.000272
South Asian	0.000131	0.000131
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). {ECO:0000250}.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.827
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.285
• hipred: Y
• hipred_score: 0.526
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppil4

Gene ontology

• Biological process: protein peptidyl-prolyl isomerization;regulation of phosphorylation of RNA polymerase II C-terminal domain
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: RNA binding;peptidyl-prolyl cis-trans isomerase activity