MARVELD3
Basic information
Region (hg38): 16:71626161-71642114
Previous symbols: [ "MRVLDC3" ]
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 MARVELD3 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.
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 | 0 | |||||
| missense | 23 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 23 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MARVELD3 | protein_coding | protein_coding | ENST00000299952 | 3 | 15954 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.59e-7 | 0.507 | 125715 | 0 | 32 | 125747 | 0.000127 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.365 | 243 | 260 | 0.936 | 0.0000150 | 2582 |
| Missense in Polyphen | 83 | 88.965 | 0.93295 | 921 | ||
| Synonymous | -0.484 | 119 | 112 | 1.06 | 0.00000714 | 897 |
| Loss of Function | 0.871 | 12 | 15.7 | 0.763 | 8.49e-7 | 159 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000366 | 0.000326 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000152 | 0.000141 |
| Middle Eastern | 0.000366 | 0.000326 |
| South Asian | 0.000276 | 0.000261 |
| Other | 0.000403 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: As a component of tight junctions, plays a role in paracellular ion conductivity. {ECO:0000269|PubMed:20028514}.;
- Pathway
- Tight junction - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.0818
Intolerance Scores
- loftool
- 0.376
- rvis_EVS
- 0.07
- rvis_percentile_EVS
- 58.96
Haploinsufficiency Scores
- pHI
- 0.355
- hipred
- N
- hipred_score
- 0.180
- ghis
- 0.397
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.332
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Marveld3
- Phenotype
Gene ontology
- Biological process
- response to osmotic stress;negative regulation of epithelial cell migration;cell-cell junction organization;negative regulation of JNK cascade;negative regulation of epithelial cell proliferation;bicellular tight junction assembly;protein localization to cell junction
- Cellular component
- bicellular tight junction;integral component of membrane;cytoplasmic vesicle
- Molecular function
- protein binding;mitogen-activated protein kinase kinase kinase binding