EPB41L3

erythrocyte membrane protein band 4.1 like 3, the group of Erythrocyte membrane protein band 4.1|FERM domain containing

Basic information

Region (hg38): 18:5392381-5630700

Links

ENSG00000082397NCBI:23136OMIM:605331HGNC:3380Uniprot:Q9Y2J2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPB41L3 gene.

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
2
clinvar
2
clinvar
4
missense
51
clinvar
3
clinvar
5
clinvar
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)2264303
18-5394754-G-C not specified Uncertain significance (Jan 23, 2024)3089411
18-5394754-G-T not specified Uncertain significance (Sep 25, 2023)3089410
18-5395134-C-T not specified Uncertain significance (May 06, 2024)3275765
18-5395655-A-T not specified Uncertain significance (Jun 07, 2023)2548015
18-5395658-G-C not specified Uncertain significance (Dec 02, 2021)2263194
18-5395678-G-T Likely benign (Aug 09, 2018)763483
18-5395685-T-G not specified Uncertain significance (Jan 06, 2023)2474313
18-5395704-C-T not specified Uncertain significance (Jul 20, 2022)2398555
18-5396233-C-T not specified Uncertain significance (Jun 20, 2024)3275766
18-5397065-T-C not specified Uncertain significance (Oct 04, 2022)2316429
18-5397074-T-C not specified Uncertain significance (Mar 01, 2023)3089409
18-5397093-T-C not specified Likely benign (Jul 20, 2021)2205415
18-5397129-G-A Benign (Jul 04, 2018)787999
18-5397140-G-A not specified Uncertain significance (Sep 28, 2021)2386159
18-5397140-G-T not specified Uncertain significance (May 21, 2024)2341349
18-5397161-A-G not specified Uncertain significance (Jan 16, 2024)3089407
18-5397182-C-T not specified Uncertain significance (May 23, 2023)2508623
18-5397206-G-A not specified Uncertain significance (Jul 06, 2021)2356486
18-5397246-C-A not specified Uncertain significance (May 20, 2024)3275769
18-5397278-G-A not specified Likely benign (Mar 24, 2023)2517638
18-5397287-G-A not specified Uncertain significance (Feb 11, 2022)2277035
18-5397297-C-T not specified Uncertain significance (Jan 17, 2024)3089406
18-5397324-C-G Benign (Jul 15, 2018)777266
18-5397333-C-T not specified Uncertain significance (Apr 01, 2024)3275760

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EPB41L3protein_codingprotein_codingENST00000341928 21238317
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00004321.001256850631257480.000251
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.485346390.8350.00003837030
Missense in Polyphen189270.840.697823111
Synonymous-0.5162832721.040.00001832169
Loss of Function4.781958.50.3250.00000320688

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007900.000771
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.0003360.000323
European (Non-Finnish)0.0002630.000255
Middle Eastern0.0001630.000163
South Asian0.0001000.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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