PIN1
peptidylprolyl cis/trans isomerase, NIMA-interacting 1, the group of Parvulins
Basic information
Region (hg38): 19:9835256-9849689
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIN1 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in PIN1
This is a list of pathogenic ClinVar variants found in the PIN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-9835366-C-T | not specified | Uncertain significance (Oct 12, 2022) | ||
| 19-9835367-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 19-9835368-G-T | not specified | Likely benign (Dec 28, 2023) | ||
| 19-9838491-C-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 19-9838492-G-A | not specified | Uncertain significance (Feb 02, 2024) | ||
| 19-9838534-G-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 19-9849126-C-T | not specified | Uncertain significance (Jun 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PIN1 | protein_coding | protein_coding | ENST00000247970 | 4 | 14426 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.740 | 0.258 | 125247 | 0 | 2 | 125249 | 0.00000798 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.35 | 66 | 105 | 0.629 | 0.00000701 | 1045 |
| Missense in Polyphen | 19 | 44.177 | 0.43009 | 384 | ||
| Synonymous | 0.407 | 41 | 44.5 | 0.922 | 0.00000331 | 300 |
| Loss of Function | 2.43 | 1 | 8.78 | 0.114 | 4.60e-7 | 97 |
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) | 0.00000927 | 0.00000883 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Peptidyl-prolyl cis/trans isomerase (PPIase) that binds to and isomerizes specific phosphorylated Ser/Thr-Pro (pSer/Thr- Pro) motifs. By inducing conformational changes in a subset of phosphorylated proteins, acts as a molecular switch in multiple cellular processes (PubMed:21497122, PubMed:22033920, Ref. 21). Displays a preference for acidic residues located N-terminally to the proline bond to be isomerized. Regulates mitosis presumably by interacting with NIMA and attenuating its mitosis-promoting activity. Down-regulates kinase activity of BTK (PubMed:16644721). Can transactivate multiple oncogenes and induce centrosome amplification, chromosome instability and cell transformation. Required for the efficient dephosphorylation and recycling of RAF1 after mitogen activation (PubMed:15664191). Binds and targets PML and BCL6 for degradation in a phosphorylation-dependent manner (PubMed:17828269). Acts as a regulator of JNK cascade by binding to phosphorylated FBXW7, disrupting FBXW7 dimerization and promoting FBXW7 autoubiquitination and degradation: degradation of FBXW7 leads to subsequent stabilization of JUN (PubMed:22608923). May facilitate the ubiquitination and proteasomal degradation of RBBP8/CtIP through CUL3/KLHL15 E3 ubiquitin-protein ligase complex, hence favors DNA double-strand repair through error-prone non-homologous end joining (NHEJ) over error-free, RBBP8-mediated homologous recombination (HR) (PubMed:23623683, PubMed:27561354). {ECO:0000269|PubMed:15664191, ECO:0000269|PubMed:16644721, ECO:0000269|PubMed:17828269, ECO:0000269|PubMed:21497122, ECO:0000269|PubMed:22033920, ECO:0000269|PubMed:22608923, ECO:0000269|PubMed:23623683, ECO:0000269|PubMed:27561354}.;
- Pathway
- RIG-I-like receptor signaling pathway - Homo sapiens (human);RIG-I-like Receptor Signaling;Gene expression (Transcription);how progesterone initiates the oocyte maturation;Generic Transcription Pathway;DDX58/IFIH1-mediated induction of interferon-alpha/beta;RNA Polymerase II Transcription;PI5P Regulates TP53 Acetylation;Innate Immune System;Immune System;p73 transcription factor network;Negative regulators of DDX58/IFIH1 signaling;Regulation of TP53 Activity through Phosphorylation;C-MYC pathway;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Wnt;PDGFR-beta signaling pathway;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.400
Intolerance Scores
- loftool
- 0.508
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.953
- hipred
- Y
- hipred_score
- 0.712
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.676
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pin1
- Phenotype
- reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- pin1
- Affected structure
- apoptotic process
- Phenotype tag
- abnormal
- Phenotype quality
- increased occurrence
Gene ontology
- Biological process
- protein peptidyl-prolyl isomerization;regulation of protein phosphorylation;positive regulation of protein phosphorylation;cell cycle;regulation of mitotic nuclear division;regulation of gene expression;neuron differentiation;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of protein binding;positive regulation of protein binding;regulation of cytokinesis;negative regulation of type I interferon production;positive regulation of protein dephosphorylation;negative regulation of protein catabolic process;negative regulation of neuron apoptotic process;positive regulation of neuron apoptotic process;positive regulation of GTPase activity;positive regulation of transcription by RNA polymerase II;microtubule polymerization;synapse organization;protein stabilization;positive regulation of ubiquitin-protein transferase activity;regulation of pathway-restricted SMAD protein phosphorylation;positive regulation of cell growth involved in cardiac muscle cell development;negative regulation of ERK1 and ERK2 cascade;positive regulation of canonical Wnt signaling pathway;regulation of protein localization to nucleus;regulation of signal transduction by p53 class mediator;negative regulation of cell motility
- Cellular component
- nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol;nuclear speck;midbody;neuron projection;glutamatergic synapse;postsynaptic cytosol
- Molecular function
- peptidyl-prolyl cis-trans isomerase activity;motor activity;protein binding;beta-catenin binding;mitogen-activated protein kinase kinase binding;GTPase activating protein binding;tau protein binding;phosphoserine residue binding;phosphothreonine residue binding;phosphoprotein binding