ULK2

unc-51 like autophagy activating kinase 2, the group of Autophagy related

Basic information

Region (hg38): 17:19770829-19867936

Links

ENSG00000083290

∙ NCBI:9706 ∙ OMIM:608650 ∙ HGNC:13480 ∙ Uniprot:Q8IYT8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ULK2 gene.

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				3 clinvar	4 clinvar	7
missense		1 clinvar	118 clinvar	5 clinvar	1 clinvar	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

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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