MAP3K7

protein-coding

mitogen-activated protein kinase kinase kinase 7, the group of Mitogen-activated protein kinase kinase kinases

Gene summary

The protein encoded by this gene is a member of the serine/threonine protein kinase family. This kinase mediates the signaling transduction induced by TGF beta and morphogenetic protein (BMP), and controls a variety of cell functions including transcription regulation and apoptosis. In response to IL-1, this protein forms a kinase complex including TRAF6, MAP3K7P1/TAB1 and MAP3K7P2/TAB2; this complex is required for the activation of nuclear factor kappa B. This kinase can also activate MAPK8/JNK, MAP2K4/MKK4, and thus plays a role in the cell response to environmental stresses. Four alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

Previous symbols:
  • TAK1

MANE transcript

NM_145331.3

Inheritance

AD

ClinVar variants

P:25U:174B:70

Top phenotype

Cardiospondylocarpofacial syndrome

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr6:90,513,573-90,587,086

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~73.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cardiospondylocarpofacial syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008005

Submitter: Orphanet

frontometaphyseal dysplasiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015942

Submitter: Orphanet

frontometaphyseal dysplasia 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014935

Submitter: G2P

cardiospondylocarpofacial syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008005

Submitter: PanelApp Australia

frontometaphyseal dysplasia 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014935

Submitter: PanelApp Australia

cardiospondylocarpofacial syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008005

Submitter: Labcorp Genetics (formerly Invitae)

frontometaphyseal dysplasiaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0015942

Submitter: Illumina

frontometaphyseal dysplasia 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014935

Submitter: Labcorp Genetics (formerly Invitae)

cardiospondylocarpofacial syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008005

Submitter: Ambry Genetics

frontometaphyseal dysplasia 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014935

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Cardiospondylocarpofacial syndromeAD

Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dermatologic; Genitourinary; Musculoskeletal; Ophthalmologic

Intervention: Audiologic/Otolaryngologic; Cardiovascular

Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; The condition can involve congenital cardiac anomalies, and awareness may allow early management

Refs: 10706363; 12503106; 20186786; 25899317; 27426733; 27426734Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP3K7 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 289
Inborn genetic diseasesTotal: 56
Cardiospondylocarpofacial syndromeTotal: 22
Frontometaphyseal dysplasia 2Total: 12
MAP3K7-related disorderTotal: 10
not specifiedTotal: 6
Abnormal cardiac outputTotal: 1
Delayed skeletal maturationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145331.3. 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
7
clinvar
47
clinvar
3
clinvar
57
missense
10
clinvar
14
clinvar
150
clinvar
19
clinvar
1
clinvar
194
nonsense
3
clinvar
3
start loss
0
frameshift
3
clinvar
3
splice donor/acceptor (+/-2bp)
1
clinvar
11
clinvar
12
Total1015174664269

Highest pathogenic variant AF is 0.0000013694672

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_145331.3RefSeqNP_663304.117MANE Select
ENST00000369329.8EnsemblENSP00000358335.317MANE Select
NM_003188.4RefSeqNP_003179.116Standard
NM_145332.3RefSeqNP_663305.116Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • T cell receptor signaling pathway - Homo sapiens (human)
  • Adherens junction - Homo sapiens (human)
  • Autophagy - animal - Homo sapiens (human)
  • TNF signaling pathway - Homo sapiens (human)
  • AMPK signaling pathway - Homo sapiens (human)

Biological Process

  • activation of MAPKK activity
  • activation of MAPK activity
  • stimulatory C-type lectin receptor signaling pathway
  • positive regulation of T cell cytokine production
  • MyD88-dependent toll-like receptor signaling pathway

Molecular Function

  • magnesium ion binding
  • protein kinase activity
  • protein serine/threonine kinase activity
  • MAP kinase kinase kinase activity
  • protein binding

Cellular Component

  • nucleus
  • Ada2/Gcn5/Ada3 transcription activator complex
  • cytosol
  • plasma membrane
  • IkappaB kinase complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000369329
Coding exons
17
Length
73473
Individuals with no LoFs
125729
Homozygous LoFs
0
Heterozygous LoFs
10
Defined
125739
p
0.0000398
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.791953390.5740.00001823972
Missense (PolyPhen)36114.350.314821337
Synonymous0.2601091130.9690.000005831113
Loss of Function5.14336.50.08210.00000177441

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.000120.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000560.000053rare
South Asian0.0000700.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. Plays an important role in the cascades of cellular responses evoked by changes in the environment. Mediates signal transduction of TRAF6, various cytokines including interleukin-1 (IL-1), transforming growth factor-beta (TGFB), TGFB-related factors like BMP2 and BMP4, toll-like receptors (TLR), tumor necrosis factor receptor CD40 and B-cell receptor (BCR). Ceramides are also able to activate MAP3K7/TAK1. Once activated, acts as an upstream activator of the MKK/JNK signal transduction cascade and the p38 MAPK signal transduction cascade through the phosphorylation and activation of several MAP kinase kinases like MAP2K1/MEK1, MAP2K3/MKK3, MAP2K6/MKK6 and MAP2K7/MKK7. These MAP2Ks in turn activate p38 MAPKs, c-jun N-terminal kinases (JNKs) and I-kappa-B kinase complex (IKK). Both p38 MAPK and JNK pathways control the transcription factors activator protein-1 (AP-1), while nuclear factor-kappa B is activated by IKK. MAP3K7 activates also IKBKB and MAPK8/JNK1 in response to TRAF6 signaling and mediates BMP2- induced apoptosis. In osmotic stress signaling, plays a major role in the activation of MAPK8/JNK1, but not that of NF-kappa-B. Promotes TRIM5 capsid-specific restriction activity. {ECO:0000269|PubMed:10094049, ECO:0000269|PubMed:11460167, ECO:0000269|PubMed:12589052, ECO:0000269|PubMed:16845370, ECO:0000269|PubMed:16893890, ECO:0000269|PubMed:21512573, ECO:0000269|PubMed:8663074, ECO:0000269|PubMed:9079627}.;
Disease
DISEASE: Frontometaphyseal dysplasia 2 (FMD2) [MIM:617137]: A form of frontometaphyseal dysplasia, a progressive sclerosing skeletal dysplasia affecting the long bones and skull. Characteristic features include supraorbital hyperostosis, cranial hyperostosis, undermodeling of the small bones, flared metaphyses, and digital anomalies. Extra-skeletal manifestations include hearing loss, cardiac malformations, and stenosis, particularly of the upper airway and urinary tract. FMD2 inheritance is autosomal dominant. {ECO:0000269|PubMed:27426733}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiospondylocarpofacial syndrome (CSCF) [MIM:157800]: A syndrome characterized by growth retardation, dysmorphic facial features, brachydactyly with carpal-tarsal fusion and extensive posterior cervical vertebral synostosis, cardiac septal defects with valve dysplasia, and deafness with inner ear malformations. CSCF transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27426734}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.338

Intolerance Scores

LoFtool
0.0769
RVIS EVS
-0.43
RVIS percentile EVS
25.15

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
K
Indispensability pred.
E
Indispensability score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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