EPB41L1

erythrocyte membrane protein band 4.1 like 1, the group of Erythrocyte membrane protein band 4.1|FERM domain containing

Basic information

Region (hg38): 20:36091504-36232799

Links

ENSG00000088367NCBI:2036OMIM:602879HGNC:3378Uniprot:Q9H4G0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
  • complex neurodevelopmental disorder (Limited), mode of inheritance: AD
  • intellectual disability, autosomal dominant 11 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder, autosomal dominant 11ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic21376300

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPB41L1 gene.

  • not_specified (125 variants)
  • not_provided (53 variants)
  • Intellectual_disability,_autosomal_dominant_11 (12 variants)
  • EPB41L1-related_disorder (11 variants)
  • Intellectual_disability (3 variants)
  • Complex_neurodevelopmental_disorder (2 variants)
  • Abnormal_brain_morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPB41L1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012156.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
26
clinvar
6
clinvar
34
missense
1
clinvar
101
clinvar
22
clinvar
2
clinvar
126
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 0 1 104 48 8

Highest pathogenic variant AF is 0.00000805456

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EPB41L1protein_codingprotein_codingENST00000338074 21141296
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8770.1231257310171257480.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.943945180.7600.00003375781
Missense in Polyphen116216.230.536472487
Synonymous1.731832150.8500.00001431743
Loss of Function4.87842.10.1900.00000207516

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006210.0000615
Ashkenazi Jewish0.0001030.0000992
East Asian0.0002730.000272
Finnish0.00004650.0000462
European (Non-Finnish)0.00007930.0000791
Middle Eastern0.0002730.000272
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May function to confer stability and plasticity to neuronal membrane via multiple interactions, including the spectrin-actin-based cytoskeleton, integral membrane channels and membrane-associated guanylate kinases.;
Pathway
Splicing factor NOVA regulated synaptic proteins;Neuronal System;Neurexins and neuroligins;Trafficking of AMPA receptors;Glutamate binding, activation of AMPA receptors and synaptic plasticity;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;Protein-protein interactions at synapses;Trk receptor signaling mediated by PI3K and PLC-gamma (Consensus)

Recessive Scores

pRec
0.0936

Intolerance Scores

loftool
0.0449
rvis_EVS
-0.73
rvis_percentile_EVS
14.15

Haploinsufficiency Scores

pHI
0.113
hipred
Y
hipred_score
0.563
ghis
0.568

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.839

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Epb41l1
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); normal phenotype;

Gene ontology

Biological process
cortical actin cytoskeleton organization;actomyosin structure organization
Cellular component
cytosol;cytoskeleton;plasma membrane
Molecular function
actin binding;structural molecule activity;protein binding