MEX3C
Basic information
Region (hg38): 18:51174550-51218333
Previous symbols: [ "RKHD2" ]
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 MEX3C 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 | 1 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 1 |
Variants in MEX3C
This is a list of pathogenic ClinVar variants found in the MEX3C region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-51176819-T-C | Likely benign (Mar 02, 2018) | |||
| 18-51177019-T-C | not specified | Uncertain significance (Aug 30, 2021) | ||
| 18-51177346-C-T | not specified | Uncertain significance (Nov 09, 2021) | ||
| 18-51196775-CGCCGCCGCG-C | Benign (Dec 31, 2019) | |||
| 18-51196939-C-T | not specified | Uncertain significance (Nov 12, 2021) | ||
| 18-51197070-G-A | not specified | Uncertain significance (Aug 16, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MEX3C | protein_coding | protein_coding | ENST00000406189 | 2 | 43755 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.862 | 0.138 | 125581 | 0 | 7 | 125588 | 0.0000279 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.67 | 230 | 313 | 0.734 | 0.0000165 | 4183 |
| Missense in Polyphen | 26 | 102.48 | 0.25371 | 1144 | ||
| Synonymous | -1.31 | 141 | 123 | 1.15 | 0.00000655 | 1460 |
| Loss of Function | 3.15 | 2 | 15.3 | 0.131 | 9.67e-7 | 190 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000199 | 0.000199 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin ligase responsible for the post- transcriptional regulation of common HLA-A allotypes. Binds to the 3' UTR of HLA-A2 mRNA, and regulates its levels by promoting mRNA decay. RNA binding is sufficient to prevent translation, but ubiquitin ligase activity is required for mRNA degradation. {ECO:0000269|PubMed:22863774, ECO:0000269|PubMed:23446422}.;
- Disease
- DISEASE: Note=Genetic variations in MEX3C may be associated with susceptibility to essential hypertension. {ECO:0000269|PubMed:17015768}.;
- Pathway
- Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.400
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.56
Haploinsufficiency Scores
- pHI
- 0.632
- hipred
- Y
- hipred_score
- 0.703
- ghis
- 0.621
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0972
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mex3c
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; skeleton phenotype; respiratory system 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); limbs/digits/tail phenotype; immune system phenotype;
Gene ontology
- Biological process
- chondrocyte hypertrophy;regulation of fat cell differentiation;energy homeostasis
- Cellular component
- nucleus;cytoplasm
- Molecular function
- RNA binding;protein binding;transferase activity;metal ion binding