MAP3K7
protein-codingmitogen-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]
- TAK1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~73.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0008005
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0015942
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0014935
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0008005
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0014935
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0008005
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0015942
Submitter: Illumina
Inheritance Pattern: AD
Disease ID:MONDO:0014935
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0008005
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014935
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MAP3K7 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | 47 | 3 | 57 | ||
| missense | 10 | 14 | 150 | 19 | 1 | 194 |
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 3 | 3 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 11 | 12 | |||
| Total | 10 | 15 | 174 | 66 | 4 | 269 |
Highest pathogenic variant AF is 0.0000013694672
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_663304.1 | 17 | MANE Select | |
| Ensembl | ENSP00000358335.3 | 17 | MANE Select | |
| RefSeq | NP_003179.1 | 16 | Standard | |
| RefSeq | NP_663305.1 | 16 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.79 | 195 | 339 | 0.574 | 0.0000182 | 3972 |
| Missense (PolyPhen) | 36 | 114.35 | 0.31482 | 1337 | ||
| Synonymous | 0.260 | 109 | 113 | 0.969 | 0.00000583 | 1113 |
| Loss of Function | 5.14 | 3 | 36.5 | 0.0821 | 0.00000177 | 441 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00012 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000056 | 0.000053 | rare |
| South Asian | 0.000070 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |