NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter) AND Retinitis pigmentosa

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Dec 13, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000132636.3

Allele description [Variation Report for NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter)]

NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter)

Genes:

PHF3:PHD finger protein 3 [Gene - OMIM - HGNC]
EYS:eyes shut homolog [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter)

HGVS:

NC_000006.12:g.63721226G>T
NG_023443.2:g.1991000C>A
NG_034034.2:g.90426G>T
NM_001142800.2:c.8805C>AMANE SELECT
NM_001290259.2:c.*7518G>T
NM_001292009.2:c.8868C>A
NM_001370348.2:c.*7518G>TMANE SELECT
NM_001370349.2:c.*7518G>T
NM_001370350.2:c.*7518G>T
NM_015153.4:c.*7518G>T
NP_001136272.1:p.Tyr2935Ter
NP_001278938.1:p.Tyr2956Ter
NC_000006.11:g.64431122G>T
NM_001142800.1:c.8805C>A

Protein change:

Y2935*

Links:

dbSNP: rs527236067

NCBI 1000 Genomes Browser:

rs527236067

Molecular consequence:

NM_001290259.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370348.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370349.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370350.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_015153.4:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001142800.2:c.8805C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001292009.2:c.8868C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Retinitis pigmentosa (RP)
Synonyms:: Tapetoretinal degeneration
Identifiers:: MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000172587	Department of Ophthalmology and Visual Sciences Kyoto University	no assertion criteria provided	pathogenic	not provided	not provided
SCV001453301	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 16, 2020)	germline	clinical testing
SCV002819515	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Dec 13, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25324289, 31213501 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000172587

Department of Ophthalmology and Visual Sciences Kyoto University

no assertion criteria provided

pathogenic

not provided

SCV001453301

Natera, Inc.

no assertion criteria provided

Pathogenic
(Sep 16, 2020)

germline

clinical testing

SCV002819515

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Dec 13, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

Citations

PubMed

Comprehensive molecular diagnosis of a large cohort of Japanese retinitis pigmentosa and Usher syndrome patients by next-generation sequencing.

Oishi M, Oishi A, Gotoh N, Ogino K, Higasa K, Iida K, Makiyama Y, Morooka S, Matsuda F, Yoshimura N.

Invest Ophthalmol Vis Sci. 2014 Oct 16;55(11):7369-75. doi: 10.1167/iovs.14-15458.

PubMed [citation]

PMID:: 25324289

Genetic characteristics of retinitis pigmentosa in 1204 Japanese patients.

Koyanagi Y, Akiyama M, Nishiguchi KM, Momozawa Y, Kamatani Y, Takata S, Inai C, Iwasaki Y, Kumano M, Murakami Y, Omodaka K, Abe T, Komori S, Gao D, Hirakata T, Kurata K, Hosono K, Ueno S, Hotta Y, Murakami A, Terasaki H, Wada Y, et al.

J Med Genet. 2019 Oct;56(10):662-670. doi: 10.1136/jmedgenet-2018-105691. Epub 2019 Jun 17.

PubMed [citation]

PMID:: 31213501

Details of each submission

From Department of Ophthalmology and Visual Sciences Kyoto University, SCV000172587.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	not provided

Description

Converted during submission to Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	not provided	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV001453301.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002819515.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: EYS c.8805C>A (p.Tyr2935X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been associated with Retinosa Pigmentosa in HGMD. The variant allele was found at a frequency of 3.2e-05 in 156836 control chromosomes. c.8805C>A has been reported in the literature as a homozygous and heterozygous genotype in multiple individuals affected with Retinitis Pigmentosa (Example: Koyanagi_2019 and Oishi_2014 etc.). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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