DYRK1B

dual specificity tyrosine phosphorylation regulated kinase 1B, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 19:39825349-39834201

Links

ENSG00000105204 ∙ NCBI:9149 ∙ OMIM:604556 ∙ HGNC:3092 ∙ Uniprot:Q9Y463 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• abdominal obesity-metabolic syndrome 3 (Strong), mode of inheritance: AD
• abdominal obesity-metabolic syndrome 3 (Strong), mode of inheritance: AD
• abdominal obesity-metabolic syndrome 3 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Abdominal obesity-metabolic syndrome 3	AD	Cardiovascular	Individuals have been reported as being affected by coronary artery disease, as well as stroke/sudden death, at a relatively young age, and preventive measures and surveillance may allow early management, potentially reducing morbidity and mortality	Cardiovascular; Endocrine	24827035

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DYRK1B gene.

• not provided (1 variants)
• Abdominal obesity-metabolic syndrome 3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYRK1B 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	55	2	60
missense	1		74	9	1	85
nonsense						0
start loss						0
frameshift			3			3
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				9	1	10
non coding				9	3	12
Total	1	0	81	73	6

Highest pathogenic variant AF is 0.00000657

Variants in DYRK1B

This is a list of pathogenic ClinVar variants found in the DYRK1B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39825706-G-C		not specified • DYRK1B-related disorder	Conflicting classifications of pathogenicity (Jul 12, 2021)
19-39825707-G-C		DYRK1B-related disorder	Likely benign (Oct 29, 2022)
19-39825750-G-A		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
19-39825755-C-T		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
19-39825765-G-T		DYRK1B-related disorder	Uncertain significance (Dec 15, 2023)
19-39825766-C-A		DYRK1B-related disorder	Likely benign (Jun 04, 2019)
19-39825778-A-C		DYRK1B-related disorder	Likely benign (Dec 08, 2022)
19-39825779-G-A		DYRK1B-related disorder	Likely benign (Aug 14, 2023)
19-39825791-G-C		DYRK1B-related disorder	Uncertain significance (Apr 24, 2023)
19-39825793-C-A			Likely benign (Oct 22, 2023)
19-39825794-G-A		Abdominal obesity-metabolic syndrome 3 • Inborn genetic diseases	Uncertain significance (Mar 15, 2024)
19-39825808-A-G		DYRK1B-related disorder	Likely benign (Jun 20, 2022)
19-39825821-C-T		DYRK1B-related disorder	Likely benign (May 19, 2021)
19-39825822-G-A		DYRK1B-related disorder	Likely benign (Oct 09, 2023)
19-39825827-C-T			Uncertain significance (Aug 11, 2021)
19-39825828-G-A		DYRK1B-related disorder	Uncertain significance (May 22, 2023)
19-39825845-G-A		Inborn genetic diseases • DYRK1B-related disorder	Uncertain significance (Oct 03, 2023)
19-39825851-T-C		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
19-39825857-G-A		Abdominal obesity-metabolic syndrome 3	Uncertain significance (Jan 06, 2023)
19-39825872-G-A		DYRK1B-related disorder	Likely benign (May 04, 2022)
19-39825873-G-A		not specified • DYRK1B-related disorder	Benign/Likely benign (Dec 09, 2023)
19-39825876-G-A		Abdominal obesity-metabolic syndrome 3	Uncertain significance (Mar 12, 2021)
19-39825887-G-C		DYRK1B-related disorder	Uncertain significance (Feb 06, 2024)
19-39825910-A-T			Uncertain significance (Oct 11, 2023)
19-39825922-C-G			Likely benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYRK1B	protein_coding	protein_coding	ENST00000593685	10	8852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0310	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	282	384	0.735	0.0000255	3981
Missense in Polyphen		73	149.18	0.48934		1527
Synonymous	-0.572	178	169	1.06	0.0000114	1356
Loss of Function	3.97	3	24.0	0.125	0.00000120	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000123
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dual-specificity kinase which possesses both serine/threonine and tyrosine kinase activities. Enhances the transcriptional activity of TCF1/HNF1A and FOXO1. Inhibits epithelial cell migration. Mediates colon carcinoma cell survival in mitogen-poor environments. Inhibits the SHH and WNT1 pathways, thereby enhancing adipogenesis. In addition, promotes expression of the gluconeogenic enzyme glucose-6-phosphatase (G6PC). {ECO:0000269|PubMed:10910078, ECO:0000269|PubMed:11980910, ECO:0000269|PubMed:14500717, ECO:0000269|PubMed:24827035}.
• Disease: DISEASE: Abdominal obesity-metabolic syndrome 3 (AOMS3) [MIM:615812]: A form of abdominal obesity-metabolic syndrome, a disorder characterized by abdominal obesity, high triglycerides, low levels of high density lipoprotein cholesterol, high blood pressure, and elevated fasting glucose levels. AOMS3 is characterized by early-onset coronary artery disease, central obesity, hypertension, and diabetes. {ECO:0000269|PubMed:24827035}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: TCR;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.417
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.655
• hipred: Y
• hipred_score: 0.704
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dyrk1b
• Phenotype: immune system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: dyrk1b
• Affected structure: pharyngeal arch
• Phenotype tag: abnormal
• Phenotype quality: physical object quality

Gene ontology

• Biological process: protein phosphorylation;myoblast fusion;peptidyl-tyrosine phosphorylation;positive regulation of transcription, DNA-templated;adipose tissue development
• Cellular component: nucleus
• Molecular function: transcription coactivator activity;protein kinase activity;protein serine/threonine kinase activity;protein serine/threonine/tyrosine kinase activity;protein tyrosine kinase activity;protein binding;ATP binding