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NM_001142800.2(EYS):c.1155T>A (p.Cys385Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 9, 2019
Accession:
VCV000236447.5
Variation ID:
236447
Description:
single nucleotide variant
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NM_001142800.2(EYS):c.1155T>A (p.Cys385Ter)

Allele ID
238032
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q12
Genomic location
6: 65402507 (GRCh38) GRCh38 UCSC
6: 66112400 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.12:g.65402507A>T
NG_023443.2:g.309719T>A
NM_001142800.2:c.1155T>A MANE Select NP_001136272.1:p.Cys385Ter nonsense
... more HGVS
Protein change
C385*
Other names
-
Canonical SPDI
NC_000006.12:65402506:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (T)

Allele frequency
1000 Genomes Project 0.00060
The Genome Aggregation Database (gnomAD) 0.00064
The Genome Aggregation Database (gnomAD), exomes 0.00068
Trans-Omics for Precision Medicine (TOPMed) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00074
The Genome Aggregation Database (gnomAD) 0.00105
Links
ClinGen: CA3877854
dbSNP: rs143994166
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, single submitter May 10, 2018 RCV000225560.2
Pathogenic 2 criteria provided, single submitter Jan 3, 2018 RCV000664630.2
Pathogenic 1 criteria provided, single submitter Nov 9, 2019 RCV001205723.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EYS - - GRCh38
GRCh37
1823 2061

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jan 03, 2018)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa 25
Allele origin: unknown
Counsyl
Accession: SCV000788626.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(May 10, 2018)
criteria provided, single submitter
Method: clinical testing
Retinal dystrophy
Allele origin: germline
Blueprint Genetics
Accession: SCV001240969.1
Submitted: (Oct 15, 2019)
Comment:
My Retina Tracker patient
Evidence details
Pathogenic
(Nov 09, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001376993.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change creates a premature translational stop signal (p.Cys385*) in the EYS gene. It is expected to result in an absent or disrupted protein … (more)
Likely pathogenic
(-)
no assertion criteria provided
Method: clinical testing
Retinal dystrophy
Allele origin: germline
Centre for Genomic Medicine, Manchester,Central Manchester University Hospitals
Accession: SCV000282553.1
Submitted: (Apr 26, 2016)
Evidence details
Pathogenic
(Jan 06, 2020)
no assertion criteria provided
Method: curation
Retinitis pigmentosa 25
Allele origin: germline
Reproductive Health Research and Development,BGI Genomics
Accession: SCV001142363.1
Submitted: (Jan 06, 2020)
Evidence details
Comment:
NM_001142800.1:c.1155T>A in the EYS gene has an allele frequency of 0.006 in European (Finnish) subpopulation in the gnomAD database. The EYS c.1155T>A (p.Cys385*) variant results … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
EYS Mutations Causing Autosomal Recessive Retinitis Pigmentosa: Changes of Retinal Structure and Function with Disease Progression. McGuigan DB Genes 2017 PMID: 28704921
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
Molecular findings from 537 individuals with inherited retinal disease. Ellingford JM Journal of medical genetics 2016 PMID: 27208204
EYS is a major gene for rod-cone dystrophies in France. Audo I Human mutation 2010 PMID: 20333770
EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa. Abd El-Aziz MM Nature genetics 2008 PMID: 18836446

Text-mined citations for rs143994166...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021