GeneBe

EYS

eyes shut homolog

Basic information

Region (hg38): 6:63719980-65707226

Previous symbols: [ "C6orf180", "EGFL11", "RP25", "EGFL10", "C6orf178", "C6orf179" ]

Links

ENSG00000188107 ∙ NCBI:346007 ∙ OMIM:612424 ∙ HGNC:21555 ∙ Uniprot:Q5T1H1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • retinitis pigmentosa 25 (Strong), mode of inheritance: AR
  • retinitis pigmentosa 25 (Definitive), mode of inheritance: AR
  • retinitis pigmentosa (Supportive), mode of inheritance: AD
  • EYS-related retinopathy (Definitive), mode of inheritance: AR
  • retinitis pigmentosa 25 (Definitive), mode of inheritance: AR
  • retinitis pigmentosa (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retitinis pigmentosa 25ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic18836446; 18976725; 21069908; 21179430; 21519034; 22277662; 22302105; 22363543

ClinVar

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

  • not_provided (3945 variants)
  • Retinitis_pigmentosa_25 (1167 variants)
  • Retinal_dystrophy (410 variants)
  • Inborn_genetic_diseases (375 variants)
  • Retinitis_pigmentosa (359 variants)
  • Autosomal_recessive_retinitis_pigmentosa (163 variants)
  • not_specified (93 variants)
  • EYS-related_disorder (65 variants)
  • Retinitis_Pigmentosa,_Recessive (6 variants)
  • EYS-related_retinopathy (3 variants)
  • Macular_dystrophy (3 variants)
  • Cone-rod_dystrophy (3 variants)
  • Optic_atrophy (2 variants)
  • Visual_impairment (2 variants)
  • Central_scotoma (1 variants)
  • Electronegative_electroretinogram (1 variants)
  • Color_vision_defect (1 variants)
  • Cystoid_macular_edema (1 variants)
  • Central_areolar_choroidal_dystrophy (1 variants)
  • Horizontal_nystagmus (1 variants)
  • Stargardt_disease (1 variants)
  • Abnormal_electroretinogram (1 variants)
  • Abnormality_of_retinal_pigmentation (1 variants)
  • Rod-cone_dystrophy (1 variants)
  • See_cases (1 variants)
  • Retinitis_punctata_albescens (1 variants)
  • Blurred_vision (1 variants)
  • Retinal_detachment (1 variants)
  • Pigmentary_retinopathy (1 variants)
  • Dyschromatopsia (1 variants)
  • Abnormality_of_the_eye (1 variants)
  • Astigmatism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EYS gene is commonly pathogenic or not. These statistics are base on transcript: NM_001142800.2. 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
35
clinvar
1320
clinvar
8
clinvar
 1365
missense
11
clinvar
64
clinvar
1560
clinvar
96
clinvar
14
clinvar
 1745
nonsense
173
clinvar
148
clinvar
 321
start loss
1
 1
frameshift
287
clinvar
230
clinvar
6
clinvar
 523
splice donor/acceptor (+/-2bp)
17
clinvar
125
clinvar
1
clinvar
1
clinvar
 144
Total 488 569 1603 1417 22

Highest pathogenic variant AF is 0.00036537836

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EYSprotein_codingprotein_codingENST00000503581 401987243
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
3.72e-410.7391256700271256970.000107
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.31814411.48e+30.9770.000070320735
Missense in Polyphen323374.40.862715355
Synonymous0.6335135320.9650.00002615835
Loss of Function3.09831190.6950.000005691798

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004270.000426
Ashkenazi Jewish0.000.00
East Asian0.0002190.000217
Finnish0.000.00
European (Non-Finnish)0.00007970.0000792
Middle Eastern0.0002190.000217
South Asian0.000.00
Other0.0003300.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required to maintain the integrity of photoreceptor cells. {ECO:0000269|PubMed:18836446}.;

Recessive Scores

pRec
0.0838

Intolerance Scores

loftool
0.0537
rvis_EVS
7.74
rvis_percentile_EVS
99.93

Haploinsufficiency Scores

pHI
0.0372
hipred
N
hipred_score
0.146
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Zebrafish Information Network

Gene name
eys
Affected structure
retinal rod cell
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
skeletal muscle tissue regeneration;detection of light stimulus involved in visual perception
Cellular component
extracellular exosome
Molecular function
molecular_function;calcium ion binding