GeneBe

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

ENSG00000169136 ∙ NCBI:22809 ∙ OMIM:606398 ∙ HGNC:790 ∙ Uniprot:Q9Y2D1 ∙ 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 ATF5 gene.

  • not_specified (14 variants)
  • not_provided (2 variants)

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. These statistics are base on transcript: NM_001193646.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
14
clinvar
 14
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 14 0 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATF5protein_codingprotein_codingENST00000423777 25234
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.2920.6901256700771257470.000306
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3391781661.070.00001051700
Missense in Polyphen8587.8860.96717875
Synonymous-0.2007774.81.030.00000478630
Loss of Function1.9828.070.2485.14e-779

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002820.000279
Ashkenazi Jewish0.000.00
East Asian0.0002240.000217
Finnish0.0004930.000462
European (Non-Finnish)0.0003340.000316
Middle Eastern0.0002240.000217
South Asian0.0005060.000490
Other0.0008340.000815

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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