ULK4

unc-51 like kinase 4, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 3:41246598-41962130

Links

ENSG00000168038 ∙ NCBI:54986 ∙ OMIM:617010 ∙ HGNC:15784 ∙ Uniprot:Q96C45 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• prostate cancer (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ULK4 gene.

• Inborn genetic diseases (48 variants)
• not provided (11 variants)
• not specified (9 variants)
• Intellectual disability, moderate (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ULK4 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				5	3	8
missense			45	7	4	56
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding					2	2
Total	0	0	45	13	9

Variants in ULK4

This is a list of pathogenic ClinVar variants found in the ULK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-41246940-C-T		not specified	Uncertain significance (Jan 25, 2023)
3-41246976-C-T		not specified	Uncertain significance (Mar 21, 2022)
3-41246981-T-C		not specified	Uncertain significance (Sep 16, 2021)
3-41249491-A-T		not specified	Uncertain significance (Apr 10, 2023)
3-41249501-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-41249508-G-A		not specified	Uncertain significance (Mar 31, 2022)
3-41249520-G-A		not specified	Uncertain significance (Feb 06, 2024)
3-41398137-A-G		not specified	Uncertain significance (Apr 25, 2022)
3-41398155-T-C		not specified	Uncertain significance (Mar 06, 2023)
3-41398183-G-A		not specified	Uncertain significance (May 11, 2022)
3-41398186-T-C		not specified	Uncertain significance (Feb 12, 2024)
3-41398197-T-C		not specified	Uncertain significance (Sep 06, 2022)
3-41398242-A-G		not specified	Uncertain significance (Aug 08, 2022)
3-41455535-T-C		not specified	Uncertain significance (Jul 12, 2022)
3-41455547-G-C		not specified	Uncertain significance (Oct 05, 2023)
3-41455578-T-C			Benign (Jul 10, 2017)
3-41455585-G-C		not specified	Uncertain significance (Nov 03, 2023)
3-41463106-A-G		not specified	Uncertain significance (May 25, 2022)
3-41463164-G-C		not specified	Likely benign (Aug 21, 2023)
3-41463230-G-A		ULK4-related disorder	Likely benign (Sep 17, 2019)
3-41566033-T-A		not specified	Uncertain significance (Jun 29, 2023)
3-41566046-T-C		not specified	Uncertain significance (Feb 15, 2023)
3-41566050-C-T			Benign/Likely benign (Nov 01, 2023)
3-41566066-A-T		not specified	Uncertain significance (Oct 03, 2022)
3-41566092-A-C		not specified	Uncertain significance (May 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ULK4	protein_coding	protein_coding	ENST00000301831	36	715833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.43e-38	0.0000869	124190	6	1112	125308	0.00447

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.906	722	657	1.10	0.0000336	8260
Missense in Polyphen		167	157.83	1.0581		2081
Synonymous	-0.413	251	243	1.03	0.0000123	2465
Loss of Function	0.882	62	70.0	0.886	0.00000332	894

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00502	0.00491
Ashkenazi Jewish	0.00279	0.00278
East Asian	0.00413	0.00403
Finnish	0.00645	0.00640
European (Non-Finnish)	0.00571	0.00557
Middle Eastern	0.00413	0.00403
South Asian	0.00378	0.00366
Other	0.00366	0.00362

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the remodeling of cytoskeletal components, such as alpha-tubulin, and in this way regulates neurite branching and elongation, as well as cell motility. {ECO:0000269|PubMed:24284070}.
• Disease: DISEASE: Note=Various anomalies in ULK4 gene have been reported for several cases of schizophrenia, schizophrenia plus bipolar disorder and autism. ULK4 gene has been proposed to be a rare susceptibility risk factor for a range of psychiatric diseases including schizophrenia. {ECO:0000269|PubMed:24284070}.

Intolerance Scores

• loftool: 0.979
• rvis_EVS: 1.71
• rvis_percentile_EVS: 96.44

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.216
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ulk4
• Phenotype: craniofacial phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland 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; digestive/alimentary phenotype; immune system phenotype; skeleton phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: microtubule cytoskeleton organization;protein phosphorylation;regulation of neuron projection development;regulation of MAPK cascade;regulation of JNK cascade;regulation of protein kinase C signaling;regulation of p38MAPK cascade;regulation of neuron migration
• Molecular function: protein serine/threonine kinase activity;ATP binding