EPB41L4A

erythrocyte membrane protein band 4.1 like 4A, the group of FERM domain containing

Basic information

Region (hg38): 5:112142440-112419313

Links

ENSG00000129595 ∙ NCBI:64097 ∙ OMIM:612141 ∙ HGNC:13278 ∙ Uniprot:Q9HCS5 ∙ 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 EPB41L4A gene.

• Inborn genetic diseases (43 variants)
• not provided (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPB41L4A 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				3	2	5
missense			41	5	3	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding				1	1	2
Total	0	0	42	9	6

Variants in EPB41L4A

This is a list of pathogenic ClinVar variants found in the EPB41L4A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-112165022-T-C		not specified	Likely benign (Feb 15, 2023)
5-112165054-G-A			Benign (May 08, 2018)
5-112165089-C-G		not specified	Likely benign (Jul 14, 2021)
5-112165095-G-C		not specified	Uncertain significance (Dec 15, 2022)
5-112165127-T-C			Likely benign (Dec 31, 2019)
5-112168746-A-C		not specified	Uncertain significance (Nov 30, 2022)
5-112168749-G-T		not specified	Uncertain significance (Dec 20, 2021)
5-112168754-A-C		not specified	Uncertain significance (Dec 16, 2023)
5-112168782-C-C			Benign (Aug 16, 2018)
5-112168789-C-A		not specified	Uncertain significance (Jun 23, 2021)
5-112168812-G-C		not specified	Uncertain significance (Dec 20, 2021)
5-112168813-T-C		not specified	Uncertain significance (Sep 06, 2022)
5-112168992-T-TA			Uncertain significance (Jan 26, 2021)
5-112169017-G-C		not specified	Uncertain significance (Apr 22, 2022)
5-112169043-C-T		not specified	Uncertain significance (Jul 08, 2022)
5-112169052-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-112169066-C-T			Likely benign (Jun 11, 2018)
5-112169067-G-A		not specified	Uncertain significance (Mar 16, 2022)
5-112184037-C-T		not specified	Uncertain significance (Apr 25, 2022)
5-112184052-T-C		not specified	Uncertain significance (Apr 25, 2023)
5-112184063-T-C			Benign (Dec 31, 2019)
5-112184115-A-G		not specified	Uncertain significance (Jul 20, 2022)
5-112195690-A-T			Benign (Dec 31, 2019)
5-112204421-G-A		not specified	Uncertain significance (Mar 02, 2023)
5-112204429-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPB41L4A	protein_coding	protein_coding	ENST00000261486	23	276876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.51e-21	0.110	124624	0	175	124799	0.000701

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.26	451	382	1.18	0.0000219	4460
Missense in Polyphen		149	132.53	1.1242		1443
Synonymous	-1.54	158	135	1.17	0.00000773	1251
Loss of Function	1.46	38	49.1	0.774	0.00000277	567

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00146
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000571	0.000556
Finnish	0.000418	0.000417
European (Non-Finnish)	0.000825	0.000821
Middle Eastern	0.000571	0.000556
South Asian	0.000928	0.000915
Other	0.000662	0.000660

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.255
• rvis_EVS: 1.61
• rvis_percentile_EVS: 95.91

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.331
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epb41l4a
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: biological_process;actomyosin structure organization
• Cellular component: cellular_component;cytoplasm;cytoskeleton
• Molecular function: molecular_function;cytoskeletal protein binding