ATF1
activating transcription factor 1, the group of Basic leucine zipper proteins
Basic information
Region (hg38): 12:50763710-50821162
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 ATF1 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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 14 | 0 | 1 |
Variants in ATF1
This is a list of pathogenic ClinVar variants found in the ATF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-50764080-G-T | Benign (Feb 17, 2020) | |||
| 12-50775325-T-G | Benign (Feb 17, 2020) | |||
| 12-50780186-C-T | not specified | Uncertain significance (May 04, 2022) | ||
| 12-50795951-G-A | not specified | Uncertain significance (Mar 25, 2024) | ||
| 12-50795974-A-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 12-50795997-G-A | not specified | Uncertain significance (Jul 14, 2023) | ||
| 12-50809505-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 12-50809539-C-T | not specified | Uncertain significance (Feb 21, 2024) | ||
| 12-50809550-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| 12-50809577-A-G | not specified | Uncertain significance (Feb 27, 2024) | ||
| 12-50809588-C-T | Benign (Jul 13, 2018) | |||
| 12-50814051-G-C | not specified | Uncertain significance (Mar 24, 2023) | ||
| 12-50814175-A-G | not specified | Uncertain significance (Jun 11, 2024) | ||
| 12-50814295-T-C | not specified | Uncertain significance (Jul 13, 2021) | ||
| 12-50814296-G-C | not specified | Uncertain significance (May 17, 2023) | ||
| 12-50814319-C-T | not specified | Uncertain significance (Feb 06, 2024) | ||
| 12-50814337-T-C | not specified | Uncertain significance (Jun 28, 2023) | ||
| 12-50814372-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 12-50819693-C-G | not specified | Uncertain significance (Oct 05, 2023) | ||
| 12-50819724-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 12-50819732-G-A | not specified | Uncertain significance (Jun 02, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATF1 | protein_coding | protein_coding | ENST00000262053 | 6 | 57413 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.634 | 0.365 | 125738 | 0 | 9 | 125747 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 104 | 148 | 0.704 | 0.00000770 | 1725 |
| Missense in Polyphen | 25 | 47.395 | 0.52749 | 611 | ||
| Synonymous | 0.497 | 48 | 52.6 | 0.913 | 0.00000279 | 556 |
| Loss of Function | 3.05 | 3 | 16.3 | 0.185 | 9.26e-7 | 175 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000552 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.0000552 | 0.0000544 |
| South Asian | 0.0000333 | 0.0000327 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: This protein binds the cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), a sequence present in many viral and cellular promoters. Binds to the Tax-responsive element (TRE) of HTLV-I. Mediates PKA-induced stimulation of CRE-reporter genes. Represses the expression of FTH1 and other antioxidant detoxification genes. Triggers cell proliferation and transformation. {ECO:0000269|PubMed:18794154, ECO:0000269|PubMed:20980392}.;
- Disease
- DISEASE: Angiomatoid fibrous histiocytoma (AFH) [MIM:612160]: A distinct variant of malignant fibrous histiocytoma that typically occurs in children and adolescents and is manifest by nodular subcutaneous growth. Characteristic microscopic features include lobulated sheets of histiocyte-like cells intimately associated with areas of hemorrhage and cystic pseudovascular spaces, as well as a striking cuffing of inflammatory cells, mimicking a lymph node metastasis. Note=The gene represented in this entry may be involved in disease pathogenesis. Chromosomal aberrations involving ATF1 are found in patients with angiomatoid fibrous histiocytoma. Translocation t(12;16)(q13;p11.2) with FUS generates a chimeric ATF1/FUS protein. Translocation t(12;22)(q13;q12) with EWSR1 generates a chimeric ATF1/EWSR1 protein.;
- Pathway
- Aldosterone synthesis and secretion - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);EGF-Core;Integrated Cancer Pathway;Androgen Receptor Network in Prostate Cancer;Interleukin-11 Signaling Pathway;Myometrial Relaxation and Contraction Pathways;EGF-EGFR Signaling Pathway;Serotonin Receptor 4-6-7 and NR3C Signaling;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Signaling by Interleukins;tnf/stress related signaling;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Innate Immune System;Immune System;Nuclear Events (kinase and transcription factor activation);Signaling by NTRK1 (TRKA);CREB phosphorylation;Signaling by NTRKs;EGFR1;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;ErbB1 downstream signaling;MyD88 dependent cascade initiated on endosome;IL3;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Signaling mediated by p38-alpha and p38-beta
(Consensus)
Recessive Scores
- pRec
- 0.181
Intolerance Scores
- loftool
- 0.467
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.06
Haploinsufficiency Scores
- pHI
- 0.899
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.522
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atf1
- Phenotype
- embryo 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); normal 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); cellular phenotype;
Gene ontology
- Biological process
- positive regulation of neuron projection development;response to organic cyclic compound;response to cobalt ion;cellular protein-containing complex assembly;positive regulation of DNA replication;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;ATF1-ATF4 transcription factor complex
- 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;DNA-binding transcription factor activity;protein binding;identical protein binding;protein-containing complex binding;protein heterodimerization activity