ULK1
unc-51 like autophagy activating kinase 1, the group of Autophagy related
Basic information
Region (hg38): 12:131894622-131923150
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (160 variants)
- not_provided (17 variants)
- ULK1-related_disorder (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ULK1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003565.4. 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 | 11 | |||||
| missense | 155 | 165 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 155 | 13 | 8 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ULK1 | protein_coding | protein_coding | ENST00000321867 | 28 | 28517 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.993 | 0.00682 | 125704 | 0 | 18 | 125722 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.07 | 585 | 663 | 0.883 | 0.0000447 | 6675 |
| Missense in Polyphen | 251 | 319.9 | 0.78462 | 3071 | ||
| Synonymous | -3.57 | 379 | 300 | 1.26 | 0.0000218 | 2205 |
| Loss of Function | 5.51 | 8 | 50.1 | 0.160 | 0.00000248 | 554 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000580 | 0.0000580 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000117 | 0.000114 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/threonine-protein kinase involved in autophagy in response to starvation. Acts upstream of phosphatidylinositol 3- kinase PIK3C3 to regulate the formation of autophagophores, the precursors of autophagosomes. Part of regulatory feedback loops in autophagy: acts both as a downstream effector and negative regulator of mammalian target of rapamycin complex 1 (mTORC1) via interaction with RPTOR. Activated via phosphorylation by AMPK and also acts as a regulator of AMPK by mediating phosphorylation of AMPK subunits PRKAA1, PRKAB2 and PRKAG1, leading to negatively regulate AMPK activity. May phosphorylate ATG13/KIAA0652 and RPTOR; however such data need additional evidences. Plays a role early in neuronal differentiation and is required for granule cell axon formation. May also phosphorylate SESN2 and SQSTM1 to regulate autophagy (PubMed:25040165). {ECO:0000269|PubMed:18936157, ECO:0000269|PubMed:21460634, ECO:0000269|PubMed:21795849, ECO:0000269|PubMed:25040165}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Target Of Rapamycin (TOR) Signaling;Nanoparticle triggered autophagic cell death;PI3K-AKT-mTOR signaling pathway and therapeutic opportunities;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Senescence and Autophagy in Cancer;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Receptor Mediated Mitophagy;Mitophagy;Macroautophagy;Cellular responses to external stimuli;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;mTOR signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.143
Intolerance Scores
- loftool
- 0.315
- rvis_EVS
- -1.22
- rvis_percentile_EVS
- 5.56
Haploinsufficiency Scores
- pHI
- 0.395
- hipred
- Y
- hipred_score
- 0.663
- ghis
- 0.471
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.617
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ulk1
- Phenotype
- cellular 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); hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- autophagosome assembly;protein phosphorylation;autophagy;signal transduction;protein localization;regulation of autophagy;macroautophagy;regulation of macroautophagy;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;neuron projection regeneration;neuron projection development;negative regulation of protein complex assembly;cellular response to nutrient levels;response to starvation;protein autophosphorylation;axon extension;autophagy of host cells involved in interaction with symbiont;positive regulation of autophagosome assembly
- Cellular component
- phagophore assembly site;cytoplasm;mitochondrial outer membrane;autophagosome;endoplasmic reticulum membrane;cytosol;membrane;axon;guanyl-nucleotide exchange factor complex;phagophore assembly site membrane;recycling endosome;extrinsic component of omegasome membrane;extrinsic component of phagophore assembly site membrane;extrinsic component of autophagosome membrane;Atg1/ULK1 kinase complex
- Molecular function
- protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity;Rab GTPase binding;identical protein binding;protein-containing complex binding;GTPase binding