ATF5
activating transcription factor 5, the group of Basic leucine zipper proteins|MicroRNA protein coding host genes
Basic information
Region (hg38): 19:49928702-49933935
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF5 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 | 2 | |||||
| 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 | 2 |
Variants in ATF5
This is a list of pathogenic ClinVar variants found in the ATF5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-49930940-C-T | Benign (Feb 20, 2018) | |||
| 19-49930969-A-C | not specified | Uncertain significance (Nov 17, 2022) | ||
| 19-49930984-G-T | not specified | Uncertain significance (Jul 26, 2022) | ||
| 19-49932496-C-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 19-49932498-C-A | Benign (Feb 20, 2018) | |||
| 19-49932548-C-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 19-49932611-C-G | not specified | Uncertain significance (May 13, 2024) | ||
| 19-49932821-A-C | not specified | Uncertain significance (Sep 14, 2023) | ||
| 19-49933000-C-T | not specified | Uncertain significance (Jun 19, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATF5 | protein_coding | protein_coding | ENST00000423777 | 2 | 5234 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.292 | 0.690 | 125670 | 0 | 77 | 125747 | 0.000306 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.339 | 178 | 166 | 1.07 | 0.0000105 | 1700 |
| Missense in Polyphen | 85 | 87.886 | 0.96717 | 875 | ||
| Synonymous | -0.200 | 77 | 74.8 | 1.03 | 0.00000478 | 630 |
| Loss of Function | 1.98 | 2 | 8.07 | 0.248 | 5.14e-7 | 79 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000282 | 0.000279 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000224 | 0.000217 |
| Finnish | 0.000493 | 0.000462 |
| European (Non-Finnish) | 0.000334 | 0.000316 |
| Middle Eastern | 0.000224 | 0.000217 |
| South Asian | 0.000506 | 0.000490 |
| Other | 0.000834 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that either stimulates or represses gene transcription through binding of different DNA regulatory elements such as cAMP response element (CRE) (consensus: 5'- GTGACGT[AC][AG]-3'), ATF5-specific response element (ARE) (consensus: 5'-C[CT]TCT[CT]CCTT[AT]-3') but also the amino acid response element (AARE), present in many viral and cellular promoters. Critically involved, often in a cell type-dependent manner, in cell survival, proliferation, and differentiation (PubMed:10373550, PubMed:15358120, PubMed:21212266, PubMed:20654631). Its transcriptional activity is enhanced by CCND3 and slightly inhibited by CDK4 (PubMed:15358120). Important regulator of the cerebral cortex formation, functions in cerebral cortical neuroprogenitor cells to maintain proliferation and to block differentiation into neurons. Must be down-regulated in order for such cells to exit the cycle and differentiate (By similarity). Participates in the pathways by which SHH promotes cerebellar granule neuron progenitor cells proliferation (By similarity). Critical for survival of mature olfactory sensory neurons (OSN), directs expression of OSN-specific genes (By similarity). May be involved in osteogenic differentiation (PubMed:22442021). Promotes cell proliferation and survival by inducing the expression of EGR1 sinergistically with ELK1. Once acetylated by EP300, binds to ARE sequences on target genes promoters, such as BCL2 and EGR1 (PubMed:21791614). Plays an anti- apoptotic role through the transcriptional regulation of BCL2, this function seems to be cell type-dependent (By similarity). Cooperates with NR1I3/CAR in the transcriptional activation of CYP2B6 in liver (PubMed:18332083). In hepatic cells, represses CRE-dependent transcription and inhibits proliferation by blocking at G2/M phase (PubMed:22528486, PubMed:18701499). May act as a negative regulator of IL1B transduction pathway in liver (PubMed:24379400). Upon IL1B stimulus, cooperates with NLK to activate the transactivation activity of C/EBP subfamily members (PubMed:25512613). Besides its function of transcription factor, acts as a cofactor of CEBPB to activate CEBPA and promote adipocyte differentiation (PubMed:24216764). Regulates centrosome dynamics in a cell-cycle- and centriole-age-dependent manner. Forms 9-foci symmetrical ring scaffold around the mother centriole to control centrosome function and the interaction between centrioles and pericentriolar material (PubMed:26213385). {ECO:0000250|UniProtKB:O70191, ECO:0000250|UniProtKB:Q6P788, ECO:0000269|PubMed:10373550, ECO:0000269|PubMed:15358120, ECO:0000269|PubMed:18332083, ECO:0000269|PubMed:18701499, ECO:0000269|PubMed:20654631, ECO:0000269|PubMed:21212266, ECO:0000269|PubMed:21791614, ECO:0000269|PubMed:22442021, ECO:0000269|PubMed:22528486, ECO:0000269|PubMed:24216764, ECO:0000269|PubMed:24379400, ECO:0000269|PubMed:25512613, ECO:0000269|PubMed:26213385}.;
- Pathway
- Myometrial Relaxation and Contraction Pathways;Signaling events mediated by PRL
(Consensus)
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- loftool
- 0.697
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.74
Haploinsufficiency Scores
- pHI
- 0.548
- hipred
- N
- hipred_score
- 0.170
- ghis
- 0.455
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.928
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atf5
- Phenotype
- craniofacial phenotype; taste/olfaction phenotype; growth/size/body region 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;circadian rhythm;negative regulation of cell population proliferation;post-embryonic development;olfactory bulb interneuron development;cerebellar granule cell precursor proliferation;multicellular organism growth;negative regulation of apoptotic process;fat cell differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of centrosome cycle;negative regulation of cell cycle G2/M phase transition
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;centrosome;cytosol
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;tubulin binding;kinase binding;sequence-specific DNA binding;transcription regulatory region DNA binding