NM_001142800.2:c.2137+1G>A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePP5_Very_Strong

The NM_001142800.2(EYS):​c.2137+1G>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000358 in 1,531,944 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: 𝑓 0.00035 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00036 ( 4 hom. )

Consequence

EYS
NM_001142800.2 splice_donor, intron

Scores

4
2
1
Splicing: ADA: 1.000
2

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:19U:1

Conservation

PhyloP100: 4.27
Variant links:
Genes affected
EYS (HGNC:21555): (eyes shut homolog) The product of this gene contains multiple epidermal growth factor (EGF)-like and LamG domains. The protein is expressed in the photoreceptor layer of the retina, and the gene is mutated in autosomal recessive retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.012082671 fraction of the gene. Cryptic splice site detected, with MaxEntScore 6, offset of -36, new splice context is: ctgGTaatt. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PP5
Variant 6-65057613-C-T is Pathogenic according to our data. Variant chr6-65057613-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 421249.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-65057613-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EYSNM_001142800.2 linkc.2137+1G>A splice_donor_variant, intron_variant Intron 13 of 42 ENST00000503581.6 NP_001136272.1 Q5T1H1-1
EYSNM_001292009.2 linkc.2137+1G>A splice_donor_variant, intron_variant Intron 13 of 43 NP_001278938.1 Q5T1H1-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EYSENST00000503581.6 linkc.2137+1G>A splice_donor_variant, intron_variant Intron 13 of 42 5 NM_001142800.2 ENSP00000424243.1 Q5T1H1-1
EYSENST00000370621.7 linkc.2137+1G>A splice_donor_variant, intron_variant Intron 13 of 43 1 ENSP00000359655.3 Q5T1H1-3

Frequencies

GnomAD3 genomes
AF:
0.000355
AC:
54
AN:
152010
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000657
Gnomad ASJ
AF:
0.00894
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000250
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000743
AC:
116
AN:
156184
Hom.:
1
AF XY:
0.000689
AC XY:
57
AN XY:
82776
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000243
Gnomad ASJ exome
AF:
0.00883
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000527
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000332
Gnomad OTH exome
AF:
0.000686
GnomAD4 exome
AF:
0.000358
AC:
494
AN:
1379816
Hom.:
4
Cov.:
28
AF XY:
0.000362
AC XY:
247
AN XY:
681964
show subpopulations
Gnomad4 AFR exome
AF:
0.0000642
Gnomad4 AMR exome
AF:
0.000196
Gnomad4 ASJ exome
AF:
0.00742
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000431
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000184
Gnomad4 OTH exome
AF:
0.000820
GnomAD4 genome
AF:
0.000355
AC:
54
AN:
152128
Hom.:
0
Cov.:
32
AF XY:
0.000417
AC XY:
31
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0000482
Gnomad4 AMR
AF:
0.0000656
Gnomad4 ASJ
AF:
0.00894
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000250
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000754
Hom.:
1
Bravo
AF:
0.000359
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000943
AC:
3
ExAC
AF:
0.00102
AC:
25

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:19Uncertain:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Retinitis pigmentosa 25 Pathogenic:9Uncertain:1
Oct 11, 2020
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

May 09, 2022
Genetics and Molecular Pathology, SA Pathology
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 02, 2023
Revvity Omics, Revvity
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 06, 2020
Reproductive Health Research and Development, BGI Genomics
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: curation

NG_023443.2(NM_001142800.1):c.2137+1G>A in the EYS gene has an allele frequency of 0.009 in Ashkenazi Jewish subpopulation in the gnomAD database. This sequence change affects a donor splice site in intron 13 of the EYS gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant has been observed as homozygous in an individual affected with retinitis pigmentosa (PMID: 28704921). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PVS1; PM3_Supporting; PP4. -

Aug 01, 2019
Blueprint Genetics
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: clinical testing

We have identified this variant in >10 individuals with a retinal dystrophy clinical indication. The variant was only seen in the heterozygous state in these individuals. Further, nearly half had a LP/P variant in another gene which explained their phenotype. -

Jun 11, 2024
Illumina Laboratory Services, Illumina
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 31, 2018
Fulgent Genetics, Fulgent Genetics
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Dec 21, 2023
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with retinitis pigmentosa 25 (MIM#602772). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 123 heterozygotes, 1 homozygote). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in multiple retinitis pigmentosa individuals, including homozygotes, and is classified as likely pathogenic/pathogenic by diagnostic laboratories in ClinVar (PMIDs: 28704921, 32728228). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Mar 30, 2024
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 29, 2024
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Pathogenic:4
Oct 24, 2024
GeneDx
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Observed with a second EYS variant, phase unknown, in patients with retinitis pigmentosa in literature; however, these patients had variants in other genes that may have also contributed to the phenotype (PMID: 32728228, 33576794, 30718709); Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 30718709, 28704921, 34426522, 31589614, 31456290, 31980526, 32552793, 33576794, 32728228, 37734845, 36941944, 37644014, 31964843, 35272565, Abiib[thesis]2023, 37028505, 38465142) -

Oct 23, 2020
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 01, 2019
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Dec 02, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change affects a donor splice site in intron 13 of the EYS gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EYS are known to be pathogenic (PMID: 18836446, 20333770). This variant is present in population databases (rs199740930, gnomAD 0.9%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individual(s) with retinitis pigmentosa (PMID: 28704921, 30718709, 33576794). ClinVar contains an entry for this variant (Variation ID: 421249). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Retinitis pigmentosa Pathogenic:4
Jun 07, 2022
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: EYS c.2137+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. The variant allele was found at a frequency of 0.00074 in 156184 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is not significantly higher than expected for a pathogenic variant in EYS causing Retinitis Pigmentosa (0.00074 vs 0.0034). The variant, c.2137+1G>A, has been reported in the literature in the homozygous and compound heterozygous state in individuals affected with Retinitis Pigmentosa (example McGuigan_2017, Jespersgaard_2019, Sharon_2020, Colombo_2021). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. There have been 13 assessments for this variant submitted to ClinVar after 2014. Five classified the variant as pathogenic, seven as likely pathogenic, and one as VUS. Based on the evidence outlined above, the variant was classified as pathogenic. -

Sep 16, 2020
Natera, Inc.
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jun 23, 2019
Sharon lab, Hadassah-Hebrew University Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Apr 01, 2018
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

EYS-related disorder Pathogenic:1
Sep 28, 2024
PreventionGenetics, part of Exact Sciences
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

The EYS c.2137+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant was reported in the homozygous state or with a second potentially causative variant in several individuals with suspected retinitis pigmentosa (McGuigan et al. 2017. PubMed ID: 28704921; Cundy et al. 2020. PubMed ID: 32728228; Colombo et al. 2021. PubMed ID: 33576794). This variant is reported in 0.89% of alleles in individuals of Ashkenazi Jewish descent in gnomAD, including one homozygous individual. Variants that disrupt the consensus splice donor site in EYS are expected to be pathogenic. In ClinVar, this variant has been interpreted as likely pathogenic or pathogenic by outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/421249/). We classify this variant as likely pathogenic. -

Retinal dystrophy Pathogenic:1
Jan 01, 2023
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.38
D
BayesDel_noAF
Pathogenic
0.25
CADD
Uncertain
25
DANN
Uncertain
0.99
Eigen
Pathogenic
0.99
Eigen_PC
Pathogenic
0.81
FATHMM_MKL
Uncertain
0.97
D
GERP RS
5.6

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.94
SpliceAI score (max)
0.97
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.57
Position offset: 37
DS_DL_spliceai
0.97
Position offset: 1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs199740930; hg19: chr6-65767506; API