MAP3K3
Basic information
Region (hg38): 17:63622415-63696305
Previous symbols: [ "MEKK3" ]
Links
Phenotypes
GenCC
Source:
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 MAP3K3 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 | 5 | |||||
missense | 34 | 36 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 15 | 15 | ||||
Total | 0 | 1 | 34 | 2 | 19 |
Variants in MAP3K3
This is a list of pathogenic ClinVar variants found in the MAP3K3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-63632650-G-A | Benign (Jun 19, 2021) | |||
17-63632759-A-G | not specified | Uncertain significance (Mar 15, 2024) | ||
17-63632794-A-C | not specified | Uncertain significance (Mar 31, 2024) | ||
17-63632869-G-T | Benign (Jun 20, 2021) | |||
17-63634724-A-G | not specified | Uncertain significance (May 27, 2022) | ||
17-63634734-C-G | not specified | Uncertain significance (Jan 09, 2024) | ||
17-63634742-A-C | not specified | Uncertain significance (Jan 23, 2024) | ||
17-63634746-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
17-63634769-T-C | not specified | Uncertain significance (Aug 23, 2021) | ||
17-63634778-G-A | not specified | Uncertain significance (Nov 17, 2023) | ||
17-63634778-G-T | not specified | Uncertain significance (Apr 19, 2024) | ||
17-63645770-AACAGCATGTC-A | Benign (Jun 19, 2021) | |||
17-63652522-A-G | Benign (Jun 19, 2021) | |||
17-63652589-A-C | not specified | Uncertain significance (May 08, 2024) | ||
17-63652635-T-A | not specified | Uncertain significance (Mar 23, 2022) | ||
17-63657696-T-C | Benign (Jun 19, 2021) | |||
17-63657837-T-C | not specified | Uncertain significance (Jul 19, 2022) | ||
17-63657839-G-C | not specified | Uncertain significance (Jan 02, 2024) | ||
17-63657973-C-T | Benign (Jun 20, 2021) | |||
17-63666680-A-G | Benign (Jun 19, 2021) | |||
17-63666979-C-T | not specified | Uncertain significance (Dec 09, 2023) | ||
17-63667000-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
17-63667000-G-T | not specified | Uncertain significance (Feb 14, 2023) | ||
17-63667013-A-G | not specified | Uncertain significance (Sep 30, 2021) | ||
17-63681778-C-T | not specified | Uncertain significance (May 02, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MAP3K3 | protein_coding | protein_coding | ENST00000361357 | 17 | 73889 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.985 | 0.0147 | 125738 | 0 | 10 | 125748 | 0.0000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.04 | 293 | 409 | 0.716 | 0.0000256 | 4326 |
Missense in Polyphen | 67 | 138 | 0.48552 | 1373 | ||
Synonymous | 0.797 | 137 | 149 | 0.917 | 0.00000874 | 1261 |
Loss of Function | 4.92 | 6 | 39.3 | 0.153 | 0.00000233 | 415 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000443 | 0.0000439 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of a protein kinase signal transduction cascade. Mediates activation of the NF-kappa-B, AP1 and DDIT3 transcriptional regulators. {ECO:0000269|PubMed:12912994, ECO:0000269|PubMed:14661019, ECO:0000269|PubMed:14743216, ECO:0000269|PubMed:9006902}.;
- Pathway
- Neurotrophin signaling pathway - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);EGF-Core;IL-1 signaling pathway;TNF alpha Signaling Pathway;EBV LMP1 signaling;Structural Pathway of Interleukin 1 (IL-1);Angiopoietin Like Protein 8 Regulatory Pathway;MAPK Cascade;EGF-EGFR Signaling Pathway;Insulin Signaling;Signaling by Interleukins;mapkinase signaling pathway;Cytokine Signaling in Immune system;Interleukin-1 signaling;Immune System;IL-7 signaling;EGFR1;JAK STAT pathway and regulation;EPO signaling;TNFalpha;VEGF;TNF receptor signaling pathway ;Regulation of p38-alpha and p38-beta;p38 MAPK signaling pathway;IL1-mediated signaling events;Interleukin-1 family signaling
(Consensus)
Recessive Scores
- pRec
- 0.240
Intolerance Scores
- loftool
- 0.183
- rvis_EVS
- -1.07
- rvis_percentile_EVS
- 7.37
Haploinsufficiency Scores
- pHI
- 0.798
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.621
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.997
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Map3k3
- Phenotype
- hematopoietic system phenotype; 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); 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); embryo phenotype; immune system phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- MAPK cascade;activation of MAPKK activity;blood vessel development;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;intracellular signal transduction;positive regulation of I-kappaB kinase/NF-kappaB signaling;protein autophosphorylation;interleukin-1-mediated signaling pathway;positive regulation of cell proliferation in bone marrow;positive regulation of cell migration involved in sprouting angiogenesis;positive regulation of p38MAPK cascade;negative regulation of cellular senescence
- Cellular component
- cytoplasm;cytosol
- Molecular function
- protein kinase activity;protein serine/threonine kinase activity;MAP kinase kinase kinase activity;protein binding;ATP binding;metal ion binding