ZFP36
ZFP36 ring finger protein, the group of Zinc fingers CCCH-type
Basic information
Region (hg38): 19:39406846-39409412
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (9 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFP36 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 | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 1 |
Variants in ZFP36
This is a list of pathogenic ClinVar variants found in the ZFP36 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-39407785-C-T | not specified | Uncertain significance (Jul 05, 2023) | ||
| 19-39407827-C-T | Benign (Jul 16, 2018) | |||
| 19-39407835-C-G | not specified | Uncertain significance (Jun 05, 2023) | ||
| 19-39407837-T-C | not specified | Uncertain significance (Sep 28, 2023) | ||
| 19-39408005-C-A | not specified | Uncertain significance (May 30, 2022) | ||
| 19-39408121-C-G | not specified | Uncertain significance (Nov 29, 2023) | ||
| 19-39408124-G-A | not specified | Uncertain significance (Dec 14, 2022) | ||
| 19-39408154-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 19-39408242-C-A | not specified | Uncertain significance (Jan 18, 2022) | ||
| 19-39408273-C-G | not specified | Uncertain significance (Feb 27, 2024) | ||
| 19-39408368-G-A | not specified | Uncertain significance (Jul 13, 2022) | ||
| 19-39408434-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
| 19-39408478-C-G | not specified | Uncertain significance (Sep 28, 2022) | ||
| 19-39408610-G-A | not specified | Uncertain significance (Dec 11, 2023) | ||
| 19-39408632-C-T | not specified | Uncertain significance (Jun 17, 2022) | ||
| 19-39408655-C-A | not specified | Uncertain significance (Dec 13, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZFP36 | protein_coding | protein_coding | ENST00000597629 | 2 | 2600 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.752 | 0.246 | 125723 | 0 | 3 | 125726 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.794 | 177 | 209 | 0.846 | 0.0000127 | 2059 |
| Missense in Polyphen | 56 | 93.051 | 0.60182 | 868 | ||
| Synonymous | -0.564 | 100 | 93.1 | 1.07 | 0.00000550 | 797 |
| Loss of Function | 2.46 | 1 | 8.95 | 0.112 | 4.84e-7 | 88 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000296 | 0.0000296 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000331 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Zinc-finger RNA-binding protein that destabilizes several cytoplasmic AU-rich element (ARE)-containing mRNA transcripts by promoting their poly(A) tail removal or deadenylation, and hence provide a mechanism for attenuating protein synthesis (PubMed:9703499, PubMed:10330172, PubMed:10751406, PubMed:11279239, PubMed:12115244, PubMed:12748283, PubMed:15187101, PubMed:15634918, PubMed:17030620, PubMed:16702957, PubMed:20702587, PubMed:20221403, PubMed:21775632, PubMed:27193233, PubMed:23644599, PubMed:25815583). Acts as an 3'-untranslated region (UTR) ARE mRNA-binding adapter protein to communicate signaling events to the mRNA decay machinery (PubMed:15687258, PubMed:23644599). Recruits deadenylase CNOT7 (and probably the CCR4-NOT complex) via association with CNOT1, and hence promotes ARE-mediated mRNA deadenylation (PubMed:23644599). Functions also by recruiting components of the cytoplasmic RNA decay machinery to the bound ARE-containing mRNAs (PubMed:11719186, PubMed:12748283, PubMed:15687258, PubMed:16364915). Self regulates by destabilizing its own mRNA (PubMed:15187101). Binds to 3'-UTR ARE of numerous mRNAs and of its own mRNA (PubMed:10330172, PubMed:10751406, PubMed:12115244, PubMed:15187101, PubMed:15634918, PubMed:17030620, PubMed:16702957, PubMed:19188452, PubMed:20702587, PubMed:20221403, PubMed:21775632, PubMed:25815583). Plays a role in anti-inflammatory responses; suppresses tumor necrosis factor (TNF)-alpha production by stimulating ARE-mediated TNF-alpha mRNA decay and several other inflammatory ARE-containing mRNAs in interferon (IFN)- and/or lipopolysaccharide (LPS)-induced macrophages (By similarity). Plays also a role in the regulation of dendritic cell maturation at the post-transcriptional level, and hence operates as part of a negative feedback loop to limit the inflammatory response (PubMed:18367721). Promotes ARE-mediated mRNA decay of hypoxia- inducible factor HIF1A mRNA during the response of endothelial cells to hypoxia (PubMed:21775632). Positively regulates early adipogenesis of preadipocytes by promoting ARE-mediated mRNA decay of immediate early genes (IEGs) (By similarity). Negatively regulates hematopoietic/erythroid cell differentiation by promoting ARE-mediated mRNA decay of the transcription factor STAT5B mRNA (PubMed:20702587). Plays a role in maintaining skeletal muscle satellite cell quiescence by promoting ARE- mediated mRNA decay of the myogenic determination factor MYOD1 mRNA (By similarity). Associates also with and regulates the expression of non-ARE-containing target mRNAs at the post- transcriptional level, such as MHC class I mRNAs (PubMed:18367721). Participates in association with argonaute RISC catalytic components in the ARE-mediated mRNA decay mechanism; assists microRNA (miRNA) targeting ARE-containing mRNAs (PubMed:15766526). May also play a role in the regulation of cytoplasmic mRNA decapping; enhances decapping of ARE-containing RNAs, in vitro (PubMed:16364915). Involved in the delivery of target ARE-mRNAs to processing bodies (PBs) (PubMed:17369404). In addition to its cytosolic mRNA-decay function, affects nuclear pre-mRNA processing (By similarity). Negatively regulates nuclear poly(A)-binding protein PABPN1-stimulated polyadenylation activity on ARE-containing pre-mRNA during LPS-stimulated macrophages (By similarity). Also involved in the regulation of stress granule (SG) and P-body (PB) formation and fusion (By similarity). Plays a role in the regulation of keratinocyte proliferation, differentiation and apoptosis (PubMed:27182009). Plays a role as a tumor suppressor by inhibiting cell proliferation in breast cancer cells (PubMed:26926077). {ECO:0000250|UniProtKB:P22893, ECO:0000269|PubMed:10330172, ECO:0000269|PubMed:10751406, ECO:0000269|PubMed:11279239, ECO:0000269|PubMed:11719186, ECO:0000269|PubMed:12115244, ECO:0000269|PubMed:12748283, ECO:0000269|PubMed:15187101, ECO:0000269|PubMed:15634918, ECO:0000269|PubMed:15687258, ECO:0000269|PubMed:15766526, ECO:0000269|PubMed:16364915, ECO:0000269|PubMed:16702957, ECO:0000269|PubMed:17030620, ECO:0000269|PubMed:17369404, ECO:0000269|PubMed:18367721, ECO:0000269|PubMed:19188452, ECO:0000269|PubMed:20221403, ECO:0000269|PubMed:20702587, ECO:0000269|PubMed:21775632, ECO:0000269|PubMed:23644599, ECO:0000269|PubMed:25815583, ECO:0000269|PubMed:26926077, ECO:0000269|PubMed:27182009, ECO:0000269|PubMed:27193233, ECO:0000269|PubMed:9703499}.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Spinal Cord Injury;Preimplantation Embryo;Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA;Metabolism of RNA;ErbB1 downstream signaling;Regulation of mRNA stability by proteins that bind AU-rich elements
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.75
Haploinsufficiency Scores
- pHI
- 0.150
- hipred
- N
- hipred_score
- 0.337
- ghis
- 0.515
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Mouse Genome Informatics
- Gene name
- Zfp36
- Phenotype
- growth/size/body region 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); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;MAPK cascade;nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;nuclear-transcribed mRNA poly(A) tail shortening;mRNA catabolic process;response to wounding;regulation of keratinocyte proliferation;nuclear-transcribed mRNA catabolic process, deadenylation-independent decay;regulation of tumor necrosis factor production;negative regulation of viral transcription;miRNA mediated inhibition of translation;p38MAPK cascade;response to starvation;regulation of mRNA stability;cellular response to fibroblast growth factor stimulus;negative regulation of interleukin-2 biosynthetic process;positive regulation of fat cell differentiation;regulation of keratinocyte differentiation;negative regulation of erythrocyte differentiation;mRNA transport;positive regulation of nuclear-transcribed mRNA poly(A) tail shortening;3'-UTR-mediated mRNA destabilization;3'-UTR-mediated mRNA stabilization;cellular response to lipopolysaccharide;cellular response to tumor necrosis factor;cellular response to epidermal growth factor stimulus;cellular response to glucocorticoid stimulus;cellular response to granulocyte macrophage colony-stimulating factor stimulus;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA;regulation of keratinocyte apoptotic process;negative regulation of polynucleotide adenylyltransferase activity;positive regulation of intracellular mRNA localization;positive regulation of gene silencing by miRNA
- Cellular component
- exosome (RNase complex);P-body;nucleus;cytoplasm;cytosol;cytoplasmic stress granule;CCR4-NOT complex;RISC-loading complex;Dcp1-Dcp2 complex;ribonucleoprotein complex
- Molecular function
- DNA binding;RNA binding;single-stranded RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;AU-rich element binding;enzyme binding;protein kinase binding;C-C chemokine binding;heat shock protein binding;mRNA 3'-UTR AU-rich region binding;metal ion binding;RNA polymerase binding;14-3-3 protein binding