EPB41L5

erythrocyte membrane protein band 4.1 like 5, the group of FERM domain containing

Basic information

Region (hg38): 2:120013076-120179119

Links

ENSG00000115109 ∙ NCBI:57669 ∙ OMIM:611730 ∙ HGNC:19819 ∙ Uniprot:Q9HCM4 ∙ 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 EPB41L5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPB41L5 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
missense			40	3		43
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	6	0

Variants in EPB41L5

This is a list of pathogenic ClinVar variants found in the EPB41L5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-120019100-C-T		not specified	Uncertain significance (Apr 22, 2024)
2-120019108-A-G			Likely benign (Apr 01, 2022)
2-120019118-C-T		not specified	Uncertain significance (Feb 26, 2024)
2-120019119-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-120019128-G-A			Uncertain significance (Jul 01, 2022)
2-120019139-G-A		not specified	Uncertain significance (Jan 31, 2023)
2-120019155-G-A		not specified	Uncertain significance (Jan 24, 2023)
2-120019167-G-A		not specified	Uncertain significance (Aug 30, 2022)
2-120019172-G-A		not specified	Uncertain significance (Dec 18, 2023)
2-120019215-C-T		not specified	Uncertain significance (Feb 06, 2024)
2-120019241-A-G		not specified	Uncertain significance (Nov 29, 2023)
2-120042033-G-A		not specified	Uncertain significance (Jul 20, 2021)
2-120042090-A-G		not specified	Uncertain significance (May 04, 2022)
2-120073199-A-C		not specified	Uncertain significance (Jan 31, 2022)
2-120074112-A-G		not specified	Uncertain significance (Mar 22, 2023)
2-120074169-A-C		not specified	Uncertain significance (Dec 20, 2023)
2-120076976-C-G		not specified	Uncertain significance (Jul 19, 2023)
2-120077036-C-G		not specified	Uncertain significance (Dec 19, 2022)
2-120077047-T-C			Likely benign (Jun 01, 2022)
2-120077247-G-C		not specified	Uncertain significance (Aug 18, 2021)
2-120078497-G-C		not specified	Uncertain significance (Aug 13, 2021)
2-120091602-C-T		not specified	Uncertain significance (May 04, 2023)
2-120100270-G-A		not specified	Likely benign (Aug 10, 2021)
2-120100273-A-G		not specified	Uncertain significance (Dec 07, 2021)
2-120100279-C-G		not specified	Uncertain significance (Apr 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPB41L5	protein_coding	protein_coding	ENST00000263713	24	166115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0208	0.979	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.155	386	395	0.978	0.0000206	4788
Missense in Polyphen		116	155.44	0.74625		1837
Synonymous	-0.109	143	141	1.01	0.00000733	1399
Loss of Function	4.73	13	48.6	0.268	0.00000277	555

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000221	0.000217
South Asian	0.000199	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May contribute to the correct positioning of tight junctions during the establishment of polarity in epithelial cells. {ECO:0000269|PubMed:17920587}.
• Pathway: Endoderm Differentiation;Mesodermal Commitment Pathway;Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• loftool: 0.0844
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.48

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.443
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.349

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epb41l5
• Phenotype: digestive/alimentary 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); vision/eye phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: epb41l5
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: increased distribution

Gene ontology

• Biological process: in utero embryonic development;epithelial to mesenchymal transition;neural plate morphogenesis;apical constriction;substrate-dependent cell migration, cell attachment to substrate;ectoderm development;endoderm development;mesoderm migration involved in gastrulation;unidimensional cell growth;posttranscriptional regulation of gene expression;positive regulation of epithelial cell migration;positive regulation of epithelial to mesenchymal transition;negative regulation of cell-cell adhesion;actomyosin structure organization;negative regulation of protein binding;positive regulation of protein binding;somite rostral/caudal axis specification;axial mesoderm morphogenesis;paraxial mesoderm development;embryonic foregut morphogenesis;positive regulation of focal adhesion assembly;regulation of establishment of protein localization;left/right axis specification;cellular response to transforming growth factor beta stimulus
• Cellular component: nucleus;cytosol;cytoskeleton;plasma membrane;focal adhesion;ruffle membrane
• Molecular function: cytoskeletal protein binding;protein domain specific binding