EPB41L2

erythrocyte membrane protein band 4.1 like 2, the group of FERM domain containing|Erythrocyte membrane protein band 4.1

Basic information

Region (hg38): 6:130839346-131063322

Links

ENSG00000079819 ∙ NCBI:2037 ∙ OMIM:603237 ∙ HGNC:3379 ∙ Uniprot:O43491 ∙ 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 EPB41L2 gene.

• Inborn genetic diseases (41 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPB41L2 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	1
missense			40	1	1	42
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	2

Variants in EPB41L2

This is a list of pathogenic ClinVar variants found in the EPB41L2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-130858194-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-130863644-A-C		not specified	Uncertain significance (Nov 03, 2023)
6-130863670-T-C		not specified	Uncertain significance (Feb 05, 2024)
6-130863690-C-A		not specified	Uncertain significance (Mar 17, 2023)
6-130863705-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-130863706-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-130865558-G-A		not specified	Uncertain significance (Oct 05, 2023)
6-130865598-G-C		not specified	Uncertain significance (Aug 28, 2023)
6-130865625-C-T		not specified	Uncertain significance (Jul 16, 2021)
6-130869620-G-A			Benign (May 09, 2018)
6-130869636-T-A		not specified	Uncertain significance (Jan 10, 2022)
6-130869673-C-T		not specified	Uncertain significance (Dec 03, 2021)
6-130869680-G-C		not specified	Uncertain significance (Jan 08, 2024)
6-130869682-G-A		not specified	Uncertain significance (Sep 16, 2021)
6-130869697-C-T		not specified	Uncertain significance (Apr 13, 2022)
6-130869720-T-C		not specified	Uncertain significance (Jul 05, 2022)
6-130869721-T-C		not specified	Uncertain significance (Jul 05, 2022)
6-130869784-C-T		not specified	Uncertain significance (Mar 01, 2023)
6-130869825-C-T		not specified	Uncertain significance (Jan 31, 2023)
6-130869826-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-130869880-C-T		not specified	Uncertain significance (Mar 14, 2023)
6-130869888-C-T		not specified	Uncertain significance (May 03, 2023)
6-130869913-C-T		not specified	Uncertain significance (Oct 06, 2023)
6-130869931-C-G		not specified	Uncertain significance (Jan 26, 2022)
6-130869940-T-C		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPB41L2	protein_coding	protein_coding	ENST00000337057	18	223976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00682	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.688	503	548	0.917	0.0000303	6586
Missense in Polyphen		253	313.05	0.80819		3807
Synonymous	-0.0600	204	203	1.01	0.0000115	1918
Loss of Function	5.51	8	50.1	0.160	0.00000242	639

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.0000544	0.0000544
South Asian	0.000170	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for dynein-dynactin complex and NUMA1 recruitment at the mitotic cell cortex during anaphase (PubMed:23870127). {ECO:0000269|PubMed:23870127}.
• Pathway: Splicing factor NOVA regulated synaptic proteins;Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.0229
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.63

Haploinsufficiency Scores

• pHI: 0.510
• hipred: Y
• hipred_score: 0.543
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.698

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Epb41l2
• Phenotype: endocrine/exocrine gland phenotype; normal phenotype; reproductive system phenotype; 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: cell cycle;cortical actin cytoskeleton organization;actomyosin structure organization;cell division;positive regulation of protein localization to cell cortex
• Cellular component: nucleus;nucleoplasm;cytosol;plasma membrane;focal adhesion;spectrin;COP9 signalosome;cell junction;extracellular exosome;cell cortex region
• Molecular function: actin binding;structural molecule activity;protein binding;spectrin binding;PH domain binding