MAP3K13

mitogen-activated protein kinase kinase kinase 13, the group of Mitogen-activated protein kinase kinase kinases

Basic information

Region (hg38): 3:185282940-185489094

Links

ENSG00000073803 ∙ NCBI:9175 ∙ OMIM:604915 ∙ HGNC:6852 ∙ Uniprot:O43283 ∙ 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 MAP3K13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP3K13 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			48	4		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	4	1

Variants in MAP3K13

This is a list of pathogenic ClinVar variants found in the MAP3K13 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-185428594-C-G		not specified	Uncertain significance (Jun 19, 2024)
3-185428625-A-G		not specified	Uncertain significance (Feb 14, 2023)
3-185428639-G-A		not specified	Uncertain significance (Oct 12, 2021)
3-185428711-G-A			Likely benign (Nov 01, 2022)
3-185428739-G-A		not specified	Likely benign (Jul 11, 2023)
3-185428753-G-A		not specified	Uncertain significance (Feb 10, 2023)
3-185428815-C-A		not specified	Uncertain significance (Apr 07, 2022)
3-185428831-G-A		not specified	Uncertain significance (Sep 23, 2023)
3-185428868-C-T		not specified	Uncertain significance (Jul 28, 2021)
3-185428870-G-T		not specified	Uncertain significance (Jun 22, 2024)
3-185428892-C-T		not specified	Uncertain significance (Nov 09, 2023)
3-185428939-T-A		not specified	Uncertain significance (Dec 13, 2023)
3-185437482-C-A		not specified	Uncertain significance (Sep 21, 2023)
3-185437560-G-C		not specified	Uncertain significance (May 25, 2023)
3-185437579-C-T		not specified	Uncertain significance (Oct 12, 2022)
3-185443456-C-T		not specified	Uncertain significance (Jun 03, 2022)
3-185447913-C-T		not specified	Uncertain significance (May 23, 2023)
3-185449954-T-A		not specified	Uncertain significance (Jul 20, 2021)
3-185451319-G-A		not specified	Uncertain significance (Mar 15, 2024)
3-185451363-G-A		not specified	Uncertain significance (Jul 13, 2022)
3-185463554-A-C		not specified	Uncertain significance (Dec 14, 2023)
3-185463617-G-A		not specified	Uncertain significance (Jun 23, 2023)
3-185465753-G-A			Benign (Mar 29, 2018)
3-185465769-C-A		not specified	Uncertain significance (Sep 22, 2023)
3-185465791-G-A		not specified	Uncertain significance (Dec 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP3K13	protein_coding	protein_coding	ENST00000265026	13	206157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.801	0.199	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.19	410	555	0.738	0.0000323	6373
Missense in Polyphen		127	210.21	0.60414		2316
Synonymous	0.654	195	207	0.942	0.0000126	1856
Loss of Function	5.19	10	49.4	0.203	0.00000311	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000215	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates the JUN N-terminal pathway through activation of the MAP kinase kinase MAP2K7. Acts synergistically with PRDX3 to regulate the activation of NF-kappa-B in the cytosol. This activation is kinase-dependent and involves activating the IKK complex, the IKBKB-containing complex that phosphorylates inhibitors of NF-kappa-B. {ECO:0000269|PubMed:11726277, ECO:0000269|PubMed:12492477, ECO:0000269|PubMed:9353328}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);EGF-Core;MAPK Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;Insulin Signaling;mapkinase signaling pathway;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;VEGF (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.331
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.2

Haploinsufficiency Scores

• pHI: 0.291
• hipred: Y
• hipred_score: 0.694
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map3k13

Gene ontology

• Biological process: MAPK cascade;activation of MAPKK activity;protein phosphorylation;JNK cascade;activation of JNKK activity;activation of JUN kinase activity;positive regulation of neuron maturation;peptidyl-serine phosphorylation;positive regulation of axon extension;protein autophosphorylation;positive regulation of NF-kappaB transcription factor activity;positive regulation of neuron projection arborization;positive regulation of branching morphogenesis of a nerve
• Cellular component: membrane
• Molecular function: protein serine/threonine kinase activity;JUN kinase kinase kinase activity;MAP kinase kinase kinase activity;protein binding;ATP binding;protein kinase binding;identical protein binding;protein homodimerization activity;metal ion binding;IkappaB kinase complex binding