ULK2
Basic information
Region (hg38): 17:19770829-19867936
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (122 variants)
- not_provided (8 variants)
- Prostate_cancer (1 variants)
- Abnormal_brain_morphology (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ULK2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014683.4. 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 | 7 | |||||
missense | 118 | 125 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 1 | 118 | 8 | 5 |
Highest pathogenic variant AF is 6.84101e-7
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ULK2 | protein_coding | protein_coding | ENST00000395544 | 27 | 97108 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.88e-8 | 1.00 | 125703 | 0 | 45 | 125748 | 0.000179 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.62 | 451 | 559 | 0.807 | 0.0000298 | 6705 |
Missense in Polyphen | 119 | 158.13 | 0.75256 | 1984 | ||
Synonymous | 0.0850 | 201 | 203 | 0.992 | 0.0000110 | 2040 |
Loss of Function | 4.03 | 23 | 55.4 | 0.415 | 0.00000302 | 661 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000441 | 0.000441 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000111 | 0.000109 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000163 | 0.000158 |
Middle Eastern | 0.000111 | 0.000109 |
South Asian | 0.000217 | 0.000196 |
Other | 0.000525 | 0.000489 |
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 a negative regulator of mammalian target of rapamycin complex 1 (mTORC1) via interaction with RPTOR. Activated via phosphorylation by AMPK, also acts as a negative regulator of AMPK through phosphorylation of the AMPK subunits PRKAA1, PRKAB2 and PRKAG1. May phosphorylate ATG13/KIAA0652, FRS2, FRS3 and RPTOR; however such data need additional evidences. Not involved in ammonia-induced autophagy or in autophagic response of cerebellar granule neurons (CGN) to low potassium concentration. Plays a role early in neuronal differentiation and is required for granule cell axon formation: may govern axon formation via Ras-like GTPase signaling and through regulation of the Rab5-mediated endocytic pathways within developing axons. {ECO:0000269|PubMed:18936157, ECO:0000269|PubMed:21460634, ECO:0000269|PubMed:21460635, ECO:0000269|PubMed:21690395, ECO:0000269|PubMed:21795849}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Target Of Rapamycin (TOR) Signaling;Nanoparticle triggered autophagic cell death;mTOR signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- 0.822
- rvis_EVS
- -1.01
- rvis_percentile_EVS
- 8.16
Haploinsufficiency Scores
- pHI
- 0.440
- hipred
- Y
- hipred_score
- 0.542
- ghis
- 0.547
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.933
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ulk2
- 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- ulk2
- Affected structure
- ventral habenular nucleus
- Phenotype tag
- abnormal
- Phenotype quality
- decreased volume
Gene ontology
- Biological process
- autophagosome assembly;autophagy;signal transduction;regulation of autophagy;response to starvation;protein autophosphorylation;negative regulation of collateral sprouting;axon extension;autophagy of host cells involved in interaction with symbiont
- Cellular component
- phagophore assembly site;cytosol;membrane;cytoplasmic vesicle membrane;phagophore assembly site membrane
- Molecular function
- protein serine/threonine kinase activity;protein binding;ATP binding