BAK1
BCL2 antagonist/killer 1, the group of BCL2 family
Basic information
Region (hg38): 6:33572546-33580293
Previous symbols: [ "CDN1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (5 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAK1 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 1 |
Variants in BAK1
This is a list of pathogenic ClinVar variants found in the BAK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-33573819-C-G | not specified | Uncertain significance (May 17, 2023) | ||
| 6-33573861-A-G | not specified | Uncertain significance (Jul 06, 2021) | ||
| 6-33574087-C-T | not specified | Uncertain significance (May 27, 2022) | ||
| 6-33574131-T-C | not specified | Likely benign (Aug 08, 2023) | ||
| 6-33574141-C-T | not specified | Uncertain significance (Nov 17, 2023) | ||
| 6-33574162-C-T | not specified | Uncertain significance (Jun 18, 2021) | ||
| 6-33574185-C-G | not specified | Uncertain significance (Nov 19, 2022) | ||
| 6-33575884-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
| 6-33575908-T-C | not specified | Uncertain significance (Mar 07, 2024) | ||
| 6-33575916-G-A | Benign (Aug 28, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BAK1 | protein_coding | protein_coding | ENST00000374467 | 5 | 7691 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000740 | 0.510 | 125720 | 0 | 28 | 125748 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.991 | 102 | 134 | 0.759 | 0.00000839 | 1357 |
| Missense in Polyphen | 26 | 31.756 | 0.81873 | 326 | ||
| Synonymous | 0.879 | 44 | 52.1 | 0.845 | 0.00000314 | 442 |
| Loss of Function | 0.670 | 9 | 11.4 | 0.786 | 5.78e-7 | 110 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000217 | 0.000217 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000880 | 0.0000879 |
| Middle Eastern | 0.000217 | 0.000217 |
| South Asian | 0.000294 | 0.000294 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the mitochondrial apoptosic process. Upon arrival of cell death signals, promotes mitochondrial outer membrane (MOM) permeabilization by oligomerizing to form pores within the MOM. This releases apoptogenic factors into the cytosol, including cytochrome c, promoting the activation of caspase 9 which in turn processes and activates the effector caspases. {ECO:0000269|PubMed:17157251, ECO:0000269|PubMed:8521816}.;
- Pathway
- Non-small cell lung cancer - Homo sapiens (human);Chronic myeloid leukemia - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Melanoma - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Apoptosis - multiple species - Homo sapiens (human);Breast cancer - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);Thyroid cancer - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Apoptosis Modulation and Signaling;Nanomaterial induced apoptosis;Apoptosis;Photodynamic therapy-induced AP-1 survival signaling.;Photodynamic therapy-induced HIF-1 survival signaling;Apoptotic Signaling Pathway;Regulation of Apoptosis by Parathyroid Hormone-related Protein;Oxidative Damage;Endometrial cancer;Chromosomal and microsatellite instability in colorectal cancer;DNA Damage Response (only ATM dependent);role of mitochondria in apoptotic signaling;Activation and oligomerization of BAK protein;Release of apoptotic factors from the mitochondria;Intrinsic Pathway for Apoptosis;Apoptosis;Programmed Cell Death;p73 transcription factor network;Direct p53 effectors
(Consensus)
Recessive Scores
- pRec
- 0.417
Intolerance Scores
- loftool
- 0.737
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.698
- ghis
- 0.590
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.984
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bak1
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; skeleton phenotype; renal/urinary system phenotype; immune system 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); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; neoplasm; reproductive system 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; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- B cell homeostasis;B cell apoptotic process;release of cytochrome c from mitochondria;blood vessel remodeling;myeloid cell homeostasis;B cell negative selection;apoptotic process;brain development;aging;mitochondrial fusion;cell population proliferation;negative regulation of cell population proliferation;intrinsic apoptotic signaling pathway in response to DNA damage;activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c;response to fungus;response to mycotoxin;response to UV-C;establishment or maintenance of transmembrane electrochemical gradient;response to gamma radiation;positive regulation of calcium ion transport into cytosol;negative regulation of gene expression;response to organic cyclic compound;endocrine pancreas development;animal organ regeneration;endoplasmic reticulum calcium ion homeostasis;negative regulation of endoplasmic reticulum calcium ion concentration;negative regulation of peptidyl-serine phosphorylation;cellular response to unfolded protein;cellular response to UV;limb morphogenesis;response to hydrogen peroxide;positive regulation of apoptotic process;regulation of protein homodimerization activity;regulation of protein heterodimerization activity;fibroblast apoptotic process;response to ethanol;positive regulation of proteolysis;regulation of mitochondrial membrane permeability;post-embryonic camera-type eye morphogenesis;regulation of cell cycle;regulation of mitochondrial membrane potential;vagina development;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;thymocyte apoptotic process;cellular response to mechanical stimulus;positive regulation of release of cytochrome c from mitochondria;apoptotic signaling pathway;extrinsic apoptotic signaling pathway in absence of ligand;activation of cysteine-type endopeptidase activity;positive regulation of endoplasmic reticulum unfolded protein response;positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;apoptotic process involved in blood vessel morphogenesis;positive regulation of IRE1-mediated unfolded protein response
- Cellular component
- mitochondrion;mitochondrial outer membrane;endoplasmic reticulum;cytosol;integral component of mitochondrial outer membrane;pore complex;BAK complex
- Molecular function
- molecular_function;protein binding;heat shock protein binding;identical protein binding;protein homodimerization activity;ion channel binding;metal ion binding;protein heterodimerization activity;chaperone binding;BH domain binding