ULK3

unc-51 like kinase 3, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 15:74836118-74843346

Links

ENSG00000140474 ∙ NCBI:25989 ∙ OMIM:613472 ∙ HGNC:19703 ∙ Uniprot:Q6PHR2 ∙ 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 ULK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ULK3 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				3	1	4
missense			34	2	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	34	5	2

Variants in ULK3

This is a list of pathogenic ClinVar variants found in the ULK3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-74837243-A-C			Benign (Feb 12, 2018)
15-74837386-G-A		not specified	Uncertain significance (Jan 26, 2023)
15-74837422-C-T		not specified	Likely benign (Dec 21, 2022)
15-74837435-T-C		not specified	Uncertain significance (Jun 28, 2022)
15-74837753-T-C		not specified	Uncertain significance (Dec 20, 2023)
15-74838171-C-T		not specified	Uncertain significance (Sep 12, 2023)
15-74838187-G-A		not specified	Uncertain significance (Dec 13, 2023)
15-74838188-C-A		not specified	Uncertain significance (Oct 03, 2022)
15-74838299-G-C		not specified	Uncertain significance (Mar 28, 2024)
15-74838316-G-A		not specified	Uncertain significance (Sep 14, 2022)
15-74838663-G-A		not specified	Uncertain significance (Feb 28, 2023)
15-74838678-A-C		not specified	Uncertain significance (Aug 02, 2023)
15-74838691-T-G		not specified	Uncertain significance (Jun 03, 2022)
15-74838721-C-T		not specified	Uncertain significance (Sep 12, 2023)
15-74838727-G-A		not specified	Uncertain significance (Jun 12, 2023)
15-74839331-C-A		not specified	Uncertain significance (Nov 17, 2023)
15-74839369-G-A		not specified	Uncertain significance (Aug 13, 2021)
15-74839558-T-C			Likely benign (Dec 01, 2022)
15-74839565-C-T		not specified	Uncertain significance (Jun 18, 2021)
15-74839590-G-T		not specified	Uncertain significance (Dec 17, 2021)
15-74839625-T-C		not specified	Uncertain significance (Mar 29, 2023)
15-74839641-G-A		not specified	Uncertain significance (Sep 12, 2023)
15-74839679-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-74839704-G-C		not specified	Uncertain significance (Sep 22, 2023)
15-74840242-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ULK3	protein_coding	protein_coding	ENST00000440863	16	7231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00203	0.998	124644	0	16	124660	0.0000642

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	215	273	0.789	0.0000171	2955
Missense in Polyphen		71	98.613	0.71999		1145
Synonymous	1.22	96	112	0.854	0.00000684	927
Loss of Function	3.28	10	29.1	0.344	0.00000155	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000157	0.000156
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000101	0.0000973
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine protein kinase that acts as a regulator of Sonic hedgehog (SHH) signaling and autophagy. Acts as a negative regulator of SHH signaling in the absence of SHH ligand: interacts with SUFU, thereby inactivating the protein kinase activity and preventing phosphorylation of GLI proteins (GLI1, GLI2 and/or GLI3). Positively regulates SHH signaling in the presence of SHH: dissociates from SUFU, autophosphorylates and mediates phosphorylation of GLI2, activating it and promoting its nuclear translocation. Phosphorylates in vitro GLI2, as well as GLI1 and GLI3, although less efficiently. Also acts as a regulator of autophagy: following cellular senescence, able to induce autophagy. {ECO:0000269|PubMed:19279323, ECO:0000269|PubMed:19878745, ECO:0000269|PubMed:20643644}.
• Pathway: Target Of Rapamycin (TOR) Signaling;Signal Transduction;Hedgehog ,on, state;Signaling by Hedgehog (Consensus)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.839
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.233
• hipred: N
• hipred_score: 0.492
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.726

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ulk3

Gene ontology

• Biological process: autophagosome assembly;autophagy;regulation of autophagy;negative regulation of smoothened signaling pathway;positive regulation of smoothened signaling pathway;protein autophosphorylation;cellular senescence
• Cellular component: phagophore assembly site;cytoplasm;cytosol;membrane;ciliary tip
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding