MAP3K19

mitogen-activated protein kinase kinase kinase 19, the group of Mitogen-activated protein kinase kinase kinases

Basic information

Region (hg38): 2:134964485-135047468

Previous symbols: [ "YSK4" ]

Links

ENSG00000176601 ∙ NCBI:80122 ∙ ∙ HGNC:26249 ∙ Uniprot:Q56UN5 ∙ 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 MAP3K19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP3K19 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				1		1
missense			46	4		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	5	0

Variants in MAP3K19

This is a list of pathogenic ClinVar variants found in the MAP3K19 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-134964875-T-C		not specified	Uncertain significance (Nov 07, 2023)
2-134964910-C-G		not specified	Uncertain significance (Dec 19, 2023)
2-134980837-G-A		not specified	Uncertain significance (May 27, 2022)
2-134980864-A-C		not specified	Uncertain significance (May 28, 2024)
2-134980893-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-134980903-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-134980951-T-C		not specified	Uncertain significance (Jan 23, 2024)
2-134981232-A-G		not specified	Uncertain significance (Nov 12, 2021)
2-134981239-T-C		not specified	Uncertain significance (Nov 07, 2023)
2-134981407-C-T		not specified	Uncertain significance (May 17, 2023)
2-134981424-C-T		not specified	Likely benign (May 26, 2024)
2-134983681-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-134983715-C-G		not specified	Uncertain significance (May 28, 2024)
2-134983719-A-G		not specified	Uncertain significance (May 13, 2024)
2-134983797-T-C		not specified	Uncertain significance (May 05, 2023)
2-134983800-T-C		not specified	Uncertain significance (Mar 15, 2024)
2-134983803-A-G		not specified	Uncertain significance (Apr 01, 2024)
2-134985852-C-G		not specified	Uncertain significance (Jun 18, 2024)
2-134985900-A-G		not specified	Uncertain significance (Nov 12, 2021)
2-134985933-A-G		not specified	Uncertain significance (Feb 21, 2024)
2-134986003-T-C		not specified	Uncertain significance (May 31, 2023)
2-134986067-C-G		not specified	Uncertain significance (Dec 07, 2021)
2-134986243-A-T		not specified	Uncertain significance (Sep 06, 2022)
2-134986265-C-A		not specified	Uncertain significance (Jan 03, 2024)
2-134986311-T-C		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP3K19	protein_coding	protein_coding	ENST00000375845	10	82978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.76e-22	0.0713	125633	0	115	125748	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	619	675	0.918	0.0000331	8851
Missense in Polyphen		129	136.89	0.94239		1807
Synonymous	-0.0235	238	238	1.00	0.0000120	2437
Loss of Function	1.43	40	51.0	0.784	0.00000276	667

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00326	0.00326
Ashkenazi Jewish	0.00	0.00
East Asian	0.00147	0.00147
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.00147	0.00147
South Asian	0.000301	0.000294
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0686

Intolerance Scores

• rvis_EVS: 2.05
• rvis_percentile_EVS: 97.78

Haploinsufficiency Scores

• pHI: 0.0864
• hipred: N
• hipred_score: 0.139
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map3k19

Gene ontology

• Biological process: signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity
• Cellular component: cytoplasm
• Molecular function: protein serine/threonine kinase activity;ATP binding