MAPKAP1
MAPK associated protein 1, the group of MTOR complex 2
Basic information
Region (hg38): 9:125437393-125707234
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAPKAP1 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 | 4 | |||||
| missense | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 15 | 1 | 4 |
Variants in MAPKAP1
This is a list of pathogenic ClinVar variants found in the MAPKAP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-125438945-T-G | not specified | Uncertain significance (Nov 08, 2022) | ||
| 9-125438992-C-T | Benign (Jun 04, 2018) | |||
| 9-125444517-T-C | not specified | Uncertain significance (Jan 23, 2024) | ||
| 9-125444576-C-T | Benign (Aug 17, 2018) | |||
| 9-125444590-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 9-125468046-C-A | not specified | Uncertain significance (Jan 16, 2024) | ||
| 9-125484539-T-C | not specified | Uncertain significance (Jun 04, 2024) | ||
| 9-125506357-G-C | not specified | Uncertain significance (Feb 28, 2024) | ||
| 9-125543111-C-T | Benign (Jul 21, 2018) | |||
| 9-125559741-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 9-125585625-C-T | not specified | Uncertain significance (Dec 02, 2022) | ||
| 9-125585694-C-G | not specified | Uncertain significance (Oct 20, 2023) | ||
| 9-125644709-G-C | Benign (Apr 29, 2020) | |||
| 9-125657739-C-G | not specified | Uncertain significance (Aug 19, 2023) | ||
| 9-125657776-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 9-125672477-T-C | not specified | Uncertain significance (Aug 12, 2022) | ||
| 9-125672480-A-G | not specified | Uncertain significance (Nov 18, 2023) | ||
| 9-125672527-C-T | Likely benign (Jul 16, 2018) | |||
| 9-125672531-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
| 9-125672544-G-C | not specified | Uncertain significance (Feb 17, 2023) | ||
| 9-125672553-T-C | not specified | Uncertain significance (Mar 28, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MAPKAP1 | protein_coding | protein_coding | ENST00000265960 | 11 | 269842 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000863 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.83 | 164 | 302 | 0.542 | 0.0000171 | 3436 |
| Missense in Polyphen | 39 | 107.47 | 0.36288 | 1212 | ||
| Synonymous | 0.784 | 111 | 122 | 0.910 | 0.00000792 | 964 |
| Loss of Function | 4.99 | 1 | 31.0 | 0.0323 | 0.00000187 | 333 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000291 | 0.0000291 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000356 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Subunit of mTORC2, which regulates cell growth and survival in response to hormonal signals. mTORC2 is activated by growth factors, but, in contrast to mTORC1, seems to be nutrient- insensitive. mTORC2 seems to function upstream of Rho GTPases to regulate the actin cytoskeleton, probably by activating one or more Rho-type guanine nucleotide exchange factors. mTORC2 promotes the serum-induced formation of stress-fibers or F-actin. mTORC2 plays a critical role in AKT1 'Ser-473' phosphorylation, which may facilitate the phosphorylation of the activation loop of AKT1 on 'Thr-308' by PDK1 which is a prerequisite for full activation. mTORC2 regulates the phosphorylation of SGK1 at 'Ser-422'. mTORC2 also modulates the phosphorylation of PRKCA on 'Ser-657'. Within mTORC2, MAPKAP1 is required for complex formation and mTORC2 kinase activity. MAPKAP1 inhibits MAP3K2 by preventing its dimerization and autophosphorylation. Inhibits HRAS and KRAS signaling. Enhances osmotic stress-induced phosphorylation of ATF2 and ATF2-mediated transcription. Involved in ciliogenesis, regulates cilia length through its interaction with CCDC28B independently of mTORC2 complex. {ECO:0000269|PubMed:15988011, ECO:0000269|PubMed:16962653, ECO:0000269|PubMed:17043309, ECO:0000269|PubMed:17054722, ECO:0000269|PubMed:17303383, ECO:0000269|PubMed:23727834}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);Target Of Rapamycin (TOR) Signaling;VEGFA-VEGFR2 Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;Steatosis AOP;Interferon type I signaling pathways;Disease;Signal Transduction;Gene expression (Transcription);VEGFA-VEGFR2 Pathway;Generic Transcription Pathway;CD28 dependent PI3K/Akt signaling;CD28 co-stimulation;Costimulation by the CD28 family;RNA Polymerase II Transcription;Immune System;Adaptive Immune System;insulin Mam;CXCR4-mediated signaling events;ErbB1 downstream signaling;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;PIP3 activates AKT signaling;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Signaling by VEGF;Constitutive Signaling by AKT1 E17K in Cancer;PI3K/AKT Signaling in Cancer;Signaling by Receptor Tyrosine Kinases;Intracellular signaling by second messengers;mTOR signaling pathway;Diseases of signal transduction;CXCR3-mediated signaling events;Class I PI3K signaling events mediated by Akt;VEGFR2 mediated vascular permeability
(Consensus)
Recessive Scores
- pRec
- 0.275
Intolerance Scores
- loftool
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.5
Haploinsufficiency Scores
- pHI
- 0.253
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.667
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mapkap1
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; vision/eye phenotype; growth/size/body region phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- mapkap1
- Affected structure
- axial mesoderm
- Phenotype tag
- abnormal
- Phenotype quality
- increased width
Gene ontology
- Biological process
- substantia nigra development;establishment or maintenance of actin cytoskeleton polarity;activation of protein kinase B activity;positive regulation of peptidyl-serine phosphorylation;TORC2 signaling;negative regulation of Ras protein signal transduction;regulation of cellular response to oxidative stress
- Cellular component
- nucleoplasm;cytoplasm;Golgi apparatus;cytosol;plasma membrane;cytoplasmic vesicle;TORC2 complex
- Molecular function
- protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;Ras GTPase binding;protein kinase binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidic acid binding;phosphatidylinositol-3,5-bisphosphate binding