ATF6B
Basic information
Region (hg38): 6:32115264-32128253
Previous symbols: [ "CREBL1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (80 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF6B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004381.5. 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 66 | 14 | 80 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 66 | 15 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ATF6B | protein_coding | protein_coding | ENST00000375203 | 18 | 30078 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.10e-7 | 0.999 | 125711 | 0 | 36 | 125747 | 0.000143 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.53 | 315 | 401 | 0.785 | 0.0000217 | 4489 |
Missense in Polyphen | 120 | 157.78 | 0.76056 | 1779 | ||
Synonymous | 1.32 | 144 | 166 | 0.870 | 0.00000870 | 1522 |
Loss of Function | 2.98 | 17 | 36.4 | 0.466 | 0.00000188 | 397 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000145 | 0.000145 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000326 | 0.000326 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000172 | 0.000158 |
Middle Eastern | 0.000326 | 0.000326 |
South Asian | 0.000164 | 0.000163 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional factor that acts in the unfolded protein response (UPR) pathway by activating UPR target genes induced during ER stress. Binds DNA on the 5'-CCAC[GA]-3' half of the ER stress response element (ERSE) (5'-CCAATN(9)CCAC[GA]-3') when NF-Y is bound to ERSE.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Cortisol synthesis and secretion - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Alcoholism - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Myometrial Relaxation and Contraction Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;G1 to S cell cycle control
(Consensus)
Intolerance Scores
- loftool
- 0.858
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 63.57
Haploinsufficiency Scores
- pHI
- 0.218
- hipred
- Y
- hipred_score
- 0.520
- ghis
- 0.504
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.824
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atf6b
- Phenotype
- cellular phenotype; hearing/vestibular/ear 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);
Gene ontology
- Biological process
- transcription, DNA-templated;signal transduction;ATF6-mediated unfolded protein response;positive regulation of transcription by RNA polymerase II;negative regulation of ATF6-mediated unfolded protein response;positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
- Cellular component
- nucleus;nucleolus;endoplasmic reticulum membrane;Golgi apparatus;integral component of endoplasmic reticulum membrane;protein-DNA complex;RNA polymerase II transcription factor complex
- Molecular function
- RNA polymerase II distal enhancer 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;cAMP response element binding;transcription regulatory region DNA binding