EZR

ezrin, the group of A-kinase anchoring proteins|FERM domain containing

Basic information

Region (hg38): 6:158765741-158819368

Previous symbols: [ "VIL2" ]

Links

ENSG00000092820 ∙ NCBI:7430 ∙ OMIM:123900 ∙ HGNC:12691 ∙ Uniprot:P15311 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EZR 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	17	5	23
missense			35	2	2	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	3	7
non coding						0
Total	0	0	36	19	7

Variants in EZR

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

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

Position	Type	Phenotype	Significance	ClinVar
6-158766935-G-A		EZR-related disorder	Likely benign (Dec 12, 2017)
6-158766974-C-T		not specified	Likely benign (Jul 19, 2023)
6-158766991-G-A		not specified	Uncertain significance (Mar 13, 2023)
6-158767020-A-T		not specified	Uncertain significance (Dec 15, 2023)
6-158767021-T-C		not specified	Uncertain significance (Dec 15, 2023)
6-158767035-CT-TC		EZR-related disorder	Uncertain significance (Nov 11, 2022)
6-158767039-T-C		EZR-related disorder	Uncertain significance (Nov 11, 2022)
6-158767050-C-T		not specified	Uncertain significance (Dec 04, 2023)
6-158767069-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-158767077-G-A		not specified	Uncertain significance (Aug 05, 2016)
6-158767271-C-T		not specified	Uncertain significance (Jun 27, 2022)
6-158767272-G-A		not specified	Uncertain significance (Mar 31, 2017)
6-158767284-C-T		not specified	Uncertain significance (Apr 05, 2023)
6-158767331-C-T		not specified	Uncertain significance (May 20, 2024)
6-158767376-G-A		not specified	Uncertain significance (Sep 27, 2022)
6-158767377-C-G			Benign (Dec 31, 2019)
6-158767393-G-C		not specified	Uncertain significance (Jun 22, 2024)
6-158767417-C-T			Likely benign (Dec 31, 2019)
6-158767423-G-A		not specified	Likely benign (Aug 30, 2019)
6-158767431-G-C		not specified	Uncertain significance (Sep 18, 2017)
6-158767435-T-A		not specified	Likely benign (Dec 31, 2019)
6-158767438-T-G		not specified	Likely benign (Jan 05, 2016)
6-158767445-G-A			Likely benign (May 16, 2018)
6-158767505-T-G		not specified	Uncertain significance (Dec 21, 2022)
6-158767507-T-C		not specified	Likely benign (Oct 20, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EZR	protein_coding	protein_coding	ENST00000367075	13	53672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.180	0.820	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.984	307	360	0.854	0.0000231	3887
Missense in Polyphen		66	115.49	0.57148		1405
Synonymous	-1.82	165	138	1.20	0.00000853	1044
Loss of Function	4.01	8	32.8	0.244	0.00000157	386

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000384	0.000381
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000798	0.0000703
Middle Eastern	0.000384	0.000381
South Asian	0.000163	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in connections of major cytoskeletal structures to the plasma membrane. In epithelial cells, required for the formation of microvilli and membrane ruffles on the apical pole. Along with PLEKHG6, required for normal macropinocytosis. {ECO:0000269|PubMed:17881735, ECO:0000269|PubMed:18270268, ECO:0000269|PubMed:19111582}.
• Pathway: Tight junction - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Pathogenic Escherichia coli infection;AGE-RAGE pathway;VEGFA-VEGFR2 Signaling Pathway;Regulation of Actin Cytoskeleton;Developmental Biology;RAGE;Recycling pathway of L1;ucalpain and friends in cell spread;cystic fibrosis transmembrane conductance regulator (cftr) and beta 2 adrenergic receptor (b2ar) pathway;mcalpain and friends in cell motility;KitReceptor;Netrin-1 signaling;L1CAM interactions;Axon guidance;FAS (CD95) signaling pathway;Syndecan-2-mediated signaling events;RhoA signaling pathway;LKB1 signaling events (Consensus)

Recessive Scores

• pRec: 0.721

Intolerance Scores

• loftool: 0.0624
• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.79

Haploinsufficiency Scores

• pHI: 0.643
• hipred: Y
• hipred_score: 0.783
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ezr
• Phenotype: growth/size/body region 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); hematopoietic system phenotype; immune system phenotype; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: ezrb
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;intestinal D-glucose absorption;sphingosine-1-phosphate receptor signaling pathway;cytoskeletal anchoring at plasma membrane;leukocyte cell-cell adhesion;axon guidance;regulation of cell shape;regulation of cell size;positive regulation of gene expression;protein kinase A signaling;gland morphogenesis;membrane to membrane docking;microvillus assembly;astral microtubule organization;actin cytoskeleton reorganization;receptor internalization;regulation of microvillus length;regulation of actin cytoskeleton organization;cellular protein-containing complex localization;positive regulation of multicellular organism growth;cortical microtubule organization;establishment of epithelial cell apical/basal polarity;filopodium assembly;phosphatidylinositol-mediated signaling;positive regulation of protein secretion;negative regulation of T cell receptor signaling pathway;actin filament bundle assembly;establishment of centrosome localization;establishment of endothelial barrier;negative regulation of ERK1 and ERK2 cascade;cellular response to cAMP;protein localization to plasma membrane;protein localization to cell cortex;negative regulation of interleukin-2 secretion;regulation of NIK/NF-kappaB signaling;regulation of organelle assembly;terminal web assembly;positive regulation of protein localization to early endosome;positive regulation of protein localization to plasma membrane;positive regulation of cellular protein catabolic process;negative regulation of p38MAPK cascade;positive regulation of early endosome to late endosome transport
• Cellular component: fibrillar center;ruffle;immunological synapse;uropod;extracellular space;cytoplasm;endosome;cytosol;actin filament;plasma membrane;microvillus;brush border;focal adhesion;actin cytoskeleton;membrane;basolateral plasma membrane;apical plasma membrane;extrinsic component of membrane;filopodium;T-tubule;cortical cytoskeleton;microvillus membrane;vesicle;ruffle membrane;protein-containing complex;ciliary basal body;cell projection;myelin sheath;cell body;microspike;plasma membrane raft;apical part of cell;perinuclear region of cytoplasm;cell tip;extracellular exosome;invadopodium;cell periphery;astrocyte projection;Schwann cell microvillus;cytoplasmic side of apical plasma membrane
• Molecular function: RNA binding;actin binding;protein binding;microtubule binding;protein C-terminus binding;protein domain specific binding;protein kinase A catalytic subunit binding;protein kinase A regulatory subunit binding;identical protein binding;S100 protein binding;cadherin binding;cell adhesion molecule binding;actin filament binding;protein kinase A binding;ATPase binding;disordered domain specific binding