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 (375 variants)
  • Retinitis pigmentosa 25 (103 variants)
  • Retinal dystrophy (60 variants)
  • Retinitis pigmentosa (42 variants)
  • EYS-related disorder (5 variants)
  • Autosomal recessive retinitis pigmentosa (3 variants)
  • Retinitis punctata albescens (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.

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
clinvar
10
clinvar
1244
clinvar
12
clinvar
 1268
missense
9
clinvar
18
clinvar
1287
clinvar
35
clinvar
26
clinvar
 1375
nonsense
156
clinvar
132
clinvar
 288
start loss
1
clinvar
 1
frameshift
236
clinvar
192
clinvar
8
clinvar
 436
inframe indel
3
clinvar
2
clinvar
21
clinvar
 26
splice donor/acceptor (+/-2bp)
16
clinvar
107
clinvar
2
clinvar
1
clinvar
 126
splice region
1
4
38
155
15
 213
non coding
3
clinvar
86
clinvar
363
clinvar
116
clinvar
 568
Total 420 456 1415 1643 154

Highest pathogenic variant AF is 0.000637

Variants in EYS

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

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

Position Type Phenotype Significance ClinVar
6-63720042-T-C Retinitis pigmentosa Uncertain significance (Jan 13, 2018)910562
6-63720048-C-T Retinitis pigmentosa Uncertain significance (Jan 13, 2018)910563
6-63720067-T-G Retinitis pigmentosa Uncertain significance (Jan 13, 2018)357682
6-63720082-T-C Retinitis pigmentosa Uncertain significance (Jan 12, 2018)910564
6-63720183-AT-A Retinitis Pigmentosa, Recessive Uncertain significance (Jun 14, 2016)357683
6-63720310-A-T Retinitis pigmentosa Uncertain significance (Jan 13, 2018)910565
6-63720318-A-G Retinitis pigmentosa Uncertain significance (Jan 13, 2018)910566
6-63720407-A-G Retinitis pigmentosa Uncertain significance (Jan 12, 2018)910567
6-63720498-T-C Retinitis Pigmentosa, Recessive Uncertain significance (Jun 14, 2016)357684
6-63720597-T-C Likely benign (Jun 12, 2023)3015254
6-63720598-A-C Uncertain significance (Aug 10, 2022)1519786
6-63720598-AT-A Uncertain significance (Oct 13, 2022)856774
6-63720599-T-C Retinal dystrophy Conflicting classifications of pathogenicity (Oct 01, 2023)2167040
6-63720601-T-TAA not specified • Retinitis pigmentosa 25 Conflicting classifications of pathogenicity (Apr 12, 2023)1065748
6-63720604-C-T Uncertain significance (Mar 11, 2022)1948618
6-63720608-A-G Likely benign (Mar 01, 2019)1129211
6-63720611-T-G Retinitis pigmentosa 25 Uncertain significance (Sep 13, 2022)1060432
6-63720614-T-C Likely benign (Dec 31, 2022)2825432
6-63720615-TCATCTC-T Uncertain significance (Jan 19, 2024)1900068
6-63720617-A-C Retinal dystrophy • Retinitis pigmentosa 25 Conflicting classifications of pathogenicity (Oct 01, 2023)964717
6-63720623-A-G Likely benign (Jun 27, 2023)1133623
6-63720626-A-G Likely benign (Jul 21, 2023)1626869
6-63720626-A-T Retinitis pigmentosa 25 • Retinal dystrophy • Retinitis pigmentosa • EYS-related disorder Pathogenic/Likely pathogenic (Mar 09, 2024)538
6-63720628-A-G Inborn genetic diseases Uncertain significance (Mar 21, 2023)2527723
6-63720628-A-AAACATTGTATCCTTCTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNAGACGGGGTTTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC Pathogenic (Mar 06, 2023)1455537

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