ATF3

activating transcription factor 3, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 1:212565334-212620777

Links

ENSG00000162772

∙ NCBI:467 ∙ OMIM:603148 ∙ HGNC:785 ∙ Uniprot:P18847 ∙ 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 ATF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF3 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				3 clinvar	1 clinvar	4
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1 clinvar	1
Total	0	0	12	3	2

Variants in ATF3

This is a list of pathogenic ClinVar variants found in the ATF3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
1-212615055-T-C	not specified	Uncertain significance (Sep 09, 2021)	2248803
1-212615079-G-A	not specified	Uncertain significance (Jun 02, 2023)	2570076
1-212615092-C-G	not specified	Uncertain significance (Sep 22, 2022)	2401400
1-212615093-C-T	ATF3-related disorder	Likely benign (May 28, 2019)	3041761
1-212615097-C-T	not specified	Uncertain significance (Sep 22, 2022)	2401401
1-212615115-G-A	not specified	Uncertain significance (Sep 22, 2023)	3130790
1-212615145-A-G	not specified	Uncertain significance (Jul 06, 2021)	2228229
1-212615180-C-T	not specified	Likely benign (Sep 14, 2023)	2602380
1-212615181-C-T	not specified	Uncertain significance (Feb 01, 2023)	2457156
1-212618131-C-T	not specified	Uncertain significance (Feb 22, 2023)	2486822
1-212618219-G-A	not specified	Likely benign (Nov 03, 2023)	3130788
1-212618229-C-G	not specified	Uncertain significance (Aug 21, 2023)	2619863
1-212619384-T-C		Benign (Oct 31, 2018)	741892
1-212619415-A-G	not specified	Uncertain significance (Jun 05, 2024)	3320432
1-212619445-C-T	not specified	Uncertain significance (Jan 04, 2024)	3130789
1-212619512-A-T	not specified	Uncertain significance (Jun 12, 2023)	2525149
1-212619521-T-C	not specified	Uncertain significance (Oct 06, 2021)	2374053
1-212619561-C-T	ATF3-related disorder	Benign (May 07, 2019)	3038017

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATF3	protein_coding	protein_coding	ENST00000341491	3	55444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0893	0.874	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.702	81	101	0.803	0.00000594	1185
Missense in Polyphen		24	37.297	0.64348		442
Synonymous	0.470	39	42.9	0.909	0.00000275	355
Loss of Function	1.79	3	8.68	0.346	6.42e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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. Represses transcription from promoters with ATF sites. It may repress transcription by stabilizing the binding of inhibitory cofactors at the promoter. Isoform 2 activates transcription presumably by sequestering inhibitory cofactors away from the promoters.;
Pathway: HTLV-I infection - Homo sapiens (human);Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;ATF4 activates genes;Myometrial Relaxation and Contraction Pathways;Photodynamic therapy-induced unfolded protein response;TGF-beta Signaling Pathway;Hypertrophy Model;ATF-2 transcription factor network;TGF_beta_Receptor;Direct p53 effectors;ID;AP-1 transcription factor network (Consensus)

Recessive Scores

pRec: 0.567

Intolerance Scores

loftool: 0.847
rvis_EVS: 0.1
rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

pHI: 0.448
hipred: Y
hipred_score: 0.800
ghis: 0.439

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Atf3
Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland 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); growth/size/body region phenotype; immune system phenotype; vision/eye 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); neoplasm; pigmentation phenotype; hematopoietic system phenotype; 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: negative regulation of transcription by RNA polymerase II;gluconeogenesis;positive regulation of cell population proliferation;cellular response to amino acid starvation;skeletal muscle cell differentiation;PERK-mediated unfolded protein response;positive regulation of transcription by RNA polymerase II;regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance;negative regulation of ERK1 and ERK2 cascade;positive regulation of TRAIL-activated apoptotic signaling pathway;positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
Cellular component: nucleus;nucleoplasm;nucleolus;CHOP-ATF3 complex
Molecular function: transcription regulatory region sequence-specific DNA binding;RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;identical protein binding;protein homodimerization activity;transcription regulatory region DNA binding;protein heterodimerization activity