GeneBe

ATF5

protein-coding

activating transcription factor 5, the group of Basic leucine zipper proteins|MicroRNA protein coding host genes

Gene summary

Enables several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and tubulin binding activity. Involved in several processes, including fat cell differentiation; regulation of DNA-templated transcription; and regulation of cell cycle process. Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001193646.2

Inheritance

—

ClinVar variants

U:19B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr19:49,928,702-49,933,935

External References & Databases

Ensembl (ENSG00000169136)NCBI Gene (22809)OMIM (606398)HGNC:790GenCCUniProt (Q9Y2D1)AlphaFoldClinVar (ATF5)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~5.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATF5 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 18
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001193646.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
 3
missense
18
clinvar
 18
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00190221
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001193646.2RefSeqNP_001180575.12MANE Select
ENST00000423777.7EnsemblENSP00000396954.12MANE Select
NM_001290746.2RefSeqNP_001277675.12Standard
NM_012068.6RefSeqNP_036200.22Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Myometrial Relaxation and Contraction Pathways
  • Signaling events mediated by PRL

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

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

Cellular Component

  • nucleus
  • nucleoplasm
  • transcription factor complex
  • centrosome
  • cytosol

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000423777
Coding exons
2
Length
5234
Individuals with no LoFs
125670
Homozygous LoFs
0
Heterozygous LoFs
77
Defined
125747
p
0.000306
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.3391781661.070.00001051700
Missense (PolyPhen)8587.8860.96717875
Synonymous-0.2007774.81.030.00000478630
Loss of Function1.9828.070.2485.14e-779

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.000160.00014rare
Ashkenazi Jewish00.0absent
East Asian0.000220.00022rare
Finnish0.000490.00046rare
European (Non-Finnish)0.000330.00032rare
South Asian0.000510.00049rare
Other0.000830.00081rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.134

Intolerance Scores

LoFtool
0.697
RVIS EVS
0.06
RVIS percentile EVS
58.74

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.928

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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