CREB3L4
cAMP responsive element binding protein 3 like 4, the group of CREB3 transcription factor family
Basic information
Region (hg38): 1:153967534-153974361
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 CREB3L4 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 | 17 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 2 | 0 |
Variants in CREB3L4
This is a list of pathogenic ClinVar variants found in the CREB3L4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153968648-G-C | not specified | Uncertain significance (Aug 26, 2022) | ||
| 1-153968691-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
| 1-153968982-A-G | not specified | Uncertain significance (May 13, 2024) | ||
| 1-153969009-C-T | not specified | Uncertain significance (Jul 30, 2023) | ||
| 1-153969060-C-G | not specified | Uncertain significance (Aug 10, 2021) | ||
| 1-153969089-C-T | not specified | Uncertain significance (Mar 23, 2022) | ||
| 1-153973011-C-T | not specified | Uncertain significance (Mar 17, 2023) | ||
| 1-153973026-G-A | not specified | Uncertain significance (Aug 02, 2023) | ||
| 1-153973229-C-G | not specified | Uncertain significance (Nov 09, 2021) | ||
| 1-153973412-C-T | not specified | Likely benign (Feb 10, 2022) | ||
| 1-153973641-C-G | not specified | Uncertain significance (Apr 08, 2024) | ||
| 1-153973670-C-G | not specified | Uncertain significance (Jul 14, 2023) | ||
| 1-153973681-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 1-153973707-C-T | not specified | Uncertain significance (Jul 08, 2022) | ||
| 1-153973892-A-T | not specified | Uncertain significance (Feb 16, 2023) | ||
| 1-153973928-G-C | not specified | Uncertain significance (Apr 19, 2024) | ||
| 1-153973961-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
| 1-153973997-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
| 1-153974022-C-T | not specified | Uncertain significance (Aug 08, 2022) | ||
| 1-153974027-G-A | not specified | Likely benign (Nov 08, 2022) | ||
| 1-153974027-G-T | not specified | Uncertain significance (Jul 05, 2022) | ||
| 1-153974042-G-A | not specified | Uncertain significance (Apr 16, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CREB3L4 | protein_coding | protein_coding | ENST00000368607 | 9 | 6830 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000514 | 0.874 | 125716 | 0 | 32 | 125748 | 0.000127 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.00511 | 221 | 221 | 0.999 | 0.0000121 | 2548 |
| Missense in Polyphen | 70 | 67.029 | 1.0443 | 876 | ||
| Synonymous | 1.26 | 75 | 90.2 | 0.831 | 0.00000487 | 817 |
| Loss of Function | 1.50 | 11 | 17.9 | 0.616 | 8.28e-7 | 201 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000213 | 0.000213 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000196 | 0.000193 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000998 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator that may play a role in the unfolded protein response. Binds to the UPR element (UPRE) but not to CRE element. Preferentially binds DNA with to the consensus sequence 5'-T[GT]ACGT[GA][GT]-3' and has transcriptional activation activity from UPRE. Binds to NF-kappa-B site and has transcriptional activation activity from NF-kappa-B-containing regulatory elements (By similarity). {ECO:0000250, ECO:0000269|PubMed:16236796}.;
- 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
(Consensus)
Recessive Scores
- pRec
- 0.0888
Intolerance Scores
- loftool
- 0.721
- rvis_EVS
- 1.4
- rvis_percentile_EVS
- 94.72
Haploinsufficiency Scores
- pHI
- 0.0451
- hipred
- N
- hipred_score
- 0.144
- ghis
- 0.382
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.319
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Creb3l4
- Phenotype
- endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- spermatogenesis;endoplasmic reticulum unfolded protein response;positive regulation of transcription by RNA polymerase II
- Cellular component
- Golgi membrane;nucleoplasm;mitochondrion;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane;nuclear membrane
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;cAMP response element binding