EPB41L3
Basic information
Region (hg38): 18:5392381-5630700
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 EPB41L3 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 | 51 | 59 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 51 | 5 | 7 |
Variants in EPB41L3
This is a list of pathogenic ClinVar variants found in the EPB41L3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
18-5394746-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
18-5394754-G-C | not specified | Uncertain significance (Jan 23, 2024) | ||
18-5394754-G-T | not specified | Uncertain significance (Sep 25, 2023) | ||
18-5395134-C-T | not specified | Uncertain significance (May 06, 2024) | ||
18-5395655-A-T | not specified | Uncertain significance (Jun 07, 2023) | ||
18-5395658-G-C | not specified | Uncertain significance (Dec 02, 2021) | ||
18-5395678-G-T | Likely benign (Aug 09, 2018) | |||
18-5395685-T-G | not specified | Uncertain significance (Jan 06, 2023) | ||
18-5395704-C-T | not specified | Uncertain significance (Jul 20, 2022) | ||
18-5396233-C-T | not specified | Uncertain significance (Jun 20, 2024) | ||
18-5397065-T-C | not specified | Uncertain significance (Oct 04, 2022) | ||
18-5397074-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
18-5397093-T-C | not specified | Likely benign (Jul 20, 2021) | ||
18-5397129-G-A | Benign (Jul 04, 2018) | |||
18-5397140-G-A | not specified | Uncertain significance (Sep 28, 2021) | ||
18-5397140-G-T | not specified | Uncertain significance (May 21, 2024) | ||
18-5397161-A-G | not specified | Uncertain significance (Jan 16, 2024) | ||
18-5397182-C-T | not specified | Uncertain significance (May 23, 2023) | ||
18-5397206-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
18-5397246-C-A | not specified | Uncertain significance (May 20, 2024) | ||
18-5397278-G-A | not specified | Likely benign (Mar 24, 2023) | ||
18-5397287-G-A | not specified | Uncertain significance (Feb 11, 2022) | ||
18-5397297-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
18-5397324-C-G | Benign (Jul 15, 2018) | |||
18-5397333-C-T | not specified | Uncertain significance (Apr 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EPB41L3 | protein_coding | protein_coding | ENST00000341928 | 21 | 238317 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000432 | 1.00 | 125685 | 0 | 63 | 125748 | 0.000251 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.48 | 534 | 639 | 0.835 | 0.0000383 | 7030 |
Missense in Polyphen | 189 | 270.84 | 0.69782 | 3111 | ||
Synonymous | -0.516 | 283 | 272 | 1.04 | 0.0000183 | 2169 |
Loss of Function | 4.78 | 19 | 58.5 | 0.325 | 0.00000320 | 688 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000790 | 0.000771 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.000336 | 0.000323 |
European (Non-Finnish) | 0.000263 | 0.000255 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000100 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Tumor suppressor that inhibits cell proliferation and promotes apoptosis. Modulates the activity of protein arginine N- methyltransferases, including PRMT3 and PRMT5. {ECO:0000269|PubMed:15334060, ECO:0000269|PubMed:15737618, ECO:0000269|PubMed:16420693, ECO:0000269|PubMed:9892180}.;
- Pathway
- Splicing factor NOVA regulated synaptic proteins;Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.204
Intolerance Scores
- loftool
- rvis_EVS
- 0.9
- rvis_percentile_EVS
- 89.33
Haploinsufficiency Scores
- pHI
- 0.491
- hipred
- Y
- hipred_score
- 0.610
- ghis
- 0.498
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.645
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Epb41l3
- 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- regulation of cell growth;protein localization to paranode region of axon;apoptotic process;cytoskeletal anchoring at plasma membrane;biological_process;regulation of cell shape;cortical cytoskeleton organization;cortical actin cytoskeleton organization;paranodal junction assembly;actomyosin structure organization;myelin maintenance;neuron projection morphogenesis;protein localization to juxtaparanode region of axon;protein localization to plasma membrane
- Cellular component
- cytosol;cytoskeleton;plasma membrane;cell-cell junction;postsynaptic density;axolemma;paranode region of axon;juxtaparanode region of axon
- Molecular function
- actin binding;structural constituent of cytoskeleton;protein binding