MAP3K4

protein-coding

mitogen-activated protein kinase kinase kinase 4, the group of Mitogen-activated protein kinase kinase kinases

Gene summary

The central core of each mitogen-activated protein kinase (MAPK) pathway is a conserved cascade of 3 protein kinases: an activated MAPK kinase kinase (MAPKKK) phosphorylates and activates a specific MAPK kinase (MAPKK), which then activates a specific MAPK. While the ERK MAPKs are activated by mitogenic stimulation, the CSBP2 and JNK MAPKs are activated by environmental stresses such as osmotic shock, UV irradiation, wound stress, and inflammatory factors. This gene encodes a MAPKKK, the MEKK4 protein, also called MTK1. This protein contains a protein kinase catalytic domain at the C terminus. The N-terminal nonkinase domain may contain a regulatory domain. Expression of MEKK4 in mammalian cells activated the CSBP2 and JNK MAPK pathways, but not the ERK pathway. In vitro kinase studies indicated that recombinant MEKK4 can specifically phosphorylate and activate PRKMK6 and SERK1, MAPKKs that activate CSBP2 and JNK, respectively but cannot phosphorylate PRKMK1, an MAPKK that activates ERKs. MEKK4 is a major mediator of environmental stresses that activate the CSBP2 MAPK pathway, and a minor mediator of the JNK pathway. Several alternatively spliced transcripts encoding distinct isoforms have been described. [provided by RefSeq, May 2014]

Previous symbols:
  • MEKK4

MANE transcript

NM_005922.4

Inheritance

—

ClinVar variants

U:208B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr6:160,991,727-161,117,385

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~125.7 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP3K4 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 191
not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005922.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
197
clinvar
6
clinvar
1
clinvar
204
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
9
clinvar
9
Total0020871216
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005922.4RefSeqNP_005913.327MANE Select
ENST00000392142.9EnsemblENSP00000375986.427MANE Select
NM_001291958.2RefSeqNP_001278887.125Standard
NM_001301072.2RefSeqNP_001288001.227Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • GnRH signaling pathway - Homo sapiens (human)
  • MAPK signaling pathway - Homo sapiens (human)
  • Intracellular Signalling Through Adenosine Receptor A2b and Adenosine
  • Intracellular Signalling Through Adenosine Receptor A2a and Adenosine
  • EGF-Core

Biological Process

  • MAPK cascade
  • activation of MAPKK activity
  • placenta development
  • response to UV-C
  • regulation of gene expression

Molecular Function

  • protein serine/threonine kinase activity
  • MAP kinase kinase kinase activity
  • protein binding
  • ATP binding
  • metal ion binding

Cellular Component

  • cytoplasm
  • perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000392142
Coding exons
27
Length
125659
Individuals with no LoFs
125715
Homozygous LoFs
0
Heterozygous LoFs
33
Defined
125748
p
0.000131
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.876538950.7300.000048510583
Missense (PolyPhen)153353.080.433334230
Synonymous-0.6433433281.050.00001883043
Loss of Function7.65985.20.1060.00000479998

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.000220.00022rare
Finnish0.0000920.000092rare
European (Non-Finnish)0.000210.00020rare
South Asian0.0000650.000065rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Component of a protein kinase signal transduction cascade. Activates the CSBP2, P38 and JNK MAPK pathways, but not the ERK pathway. Specifically phosphorylates and activates MAP2K4 and MAP2K6. {ECO:0000269|PubMed:12052864, ECO:0000269|PubMed:9305639}.;

Recessive Scores

pRec
0.114

Intolerance Scores

LoFtool
0.579
RVIS EVS
-1.08
RVIS percentile EVS
7.32

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
H
Indispensability pred.
E
Indispensability score
0.986

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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