CREB3L3
cAMP responsive element binding protein 3 like 3, the group of CREB3 transcription factor family
Basic information
Region (hg38): 19:4153631-4173054
Links
Phenotypes
GenCC
Source:
- hypertriglyceridemia (Strong), mode of inheritance: AD
- hypertriglyceridemia 1 (Limited), mode of inheritance: AD
- hypertriglyceridemia 2 (Limited), mode of inheritance: AD
- hypertriglyceridemia 2 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Hypertriglyceridemia 2 | AD | Cardiovascular | The condition can involve hypertriglyceridemia, and management via diet and omega-3 fatty acid therapy has been described as beneficial | Cardiovascular | 26427795; 29954705 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (217 variants)
- not_specified (56 variants)
- Hypertriglyceridemia_2 (10 variants)
- CREB3L3-related_disorder (8 variants)
- Hypertriglyceridemia_1 (2 variants)
- Episodic_kinesigenic_dyskinesia_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CREB3L3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032607.3. 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 | 47 | 57 | ||||
| missense | 112 | 18 | 133 | |||
| nonsense | 9 | |||||
| start loss | 0 | |||||
| frameshift | 8 | |||||
| splice donor/acceptor (+/-2bp) | 6 | |||||
| Total | 8 | 10 | 119 | 65 | 11 |
Highest pathogenic variant AF is 0.000042148742
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CREB3L3 | protein_coding | protein_coding | ENST00000078445 | 10 | 19454 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.06e-14 | 0.0187 | 125569 | 0 | 179 | 125748 | 0.000712 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.249 | 258 | 270 | 0.957 | 0.0000168 | 2950 |
| Missense in Polyphen | 74 | 81.201 | 0.91132 | 955 | ||
| Synonymous | -1.81 | 149 | 123 | 1.21 | 0.00000868 | 990 |
| Loss of Function | -0.0484 | 20 | 19.8 | 1.01 | 0.00000109 | 210 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00194 | 0.00194 |
| Ashkenazi Jewish | 0.000198 | 0.000198 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.000231 | 0.000231 |
| European (Non-Finnish) | 0.000795 | 0.000791 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.00213 | 0.00212 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that may act during endoplasmic reticulum stress by activating unfolded protein response target genes. Activated in response to cAMP stimulation. In vitro, binds to the cAMP response element (CRE) and box-B element. Activates transcription through box-B element. Activates transcription through CRE (By similarity). Seems to function synergistically with ATF6. In acute inflammatory response, may activate expression of acute phase response (APR) genes. May be involved in growth suppression. {ECO:0000250, ECO:0000269|PubMed:11353085, ECO:0000269|PubMed:15800215, ECO:0000269|PubMed:16469704}.;
- 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);Insulin resistance - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);cAMP signaling 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);Cholinergic synapse - Homo sapiens (human);Alcoholism - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;G1 to S cell cycle control;Unfolded Protein Response (UPR);Metabolism of proteins;CREB3 factors activate genes;Transport of small molecules;Assembly of active LPL and LIPC lipase complexes;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling
(Consensus)
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- loftool
- 0.262
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.67
Haploinsufficiency Scores
- pHI
- 0.0814
- hipred
- N
- hipred_score
- 0.170
- ghis
- 0.427
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.433
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Creb3l3
- 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; immune system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- positive regulation of acute inflammatory response;endoplasmic reticulum unfolded protein response;positive regulation of transcription by RNA polymerase II;positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
- Cellular component
- Golgi membrane;nucleus;nucleoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;membrane;integral component of membrane
- Molecular function
- transcription regulatory region sequence-specific DNA binding;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;protein binding;cAMP response element binding;protein homodimerization activity;protein heterodimerization activity