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): 18:5392380-5630700

Links

ENSG00000082397 ∙ NCBI:23136 ∙ OMIM:605331 ∙ HGNC:3380 ∙ Uniprot:Q9Y2J2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (46 variants)
• not provided (10 variants)

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	2	4
missense			44	3	5	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	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)
18-5395655-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)
18-5397065-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 (Mar 29, 2022)
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)
18-5397278-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)
18-5397405-A-C			Benign (Jul 04, 2018)
18-5397407-T-C		not specified	Uncertain significance (Mar 29, 2022)
18-5398050-C-A		not specified	Uncertain significance (Jun 18, 2021)
18-5398090-T-A		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

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: 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

• 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