NM_001142800.2(EYS):c.6416G>A (p.Cys2139Tyr) AND not specified

Germline classification:: no classifications from unflagged records (1 submission)
Last evaluated:: Feb 7, 2023
Review status:: no classifications from unflagged records

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:: RCV000169660.6

Allele description [Variation Report for NM_001142800.2(EYS):c.6416G>A (p.Cys2139Tyr)]

NM_001142800.2(EYS):c.6416G>A (p.Cys2139Tyr)

Gene:

EYS:eyes shut homolog [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.6416G>A (p.Cys2139Tyr)

HGVS:

NC_000006.12:g.64230600C>T
NG_023443.2:g.1481626G>A
NM_001142800.2:c.6416G>AMANE SELECT
NM_001292009.2:c.6416G>A
NP_001136272.1:p.Cys2139Tyr
NP_001278938.1:p.Cys2139Tyr
NC_000006.11:g.64940493C>T
NM_001142800.1:c.6416G>A
Q5T1H1:p.Cys2139Tyr

Protein change:

C2139Y

Links:

UniProtKB: Q5T1H1#VAR_063478; dbSNP: rs749909863

NCBI 1000 Genomes Browser:

rs749909863

Molecular consequence:

NM_001142800.2:c.6416G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001292009.2:c.6416G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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No clinical assertions found. See "Flagged submissions" below.

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Summary from all submissions

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

Citations

PubMed

EYS is a major gene for rod-cone dystrophies in France.

Audo I, Sahel JA, Mohand-Saïd S, Lancelot ME, Antonio A, Moskova-Doumanova V, Nandrot EF, Doumanov J, Barragan I, Antinolo G, Bhattacharya SS, Zeitz C.

Hum Mutat. 2010 May;31(5):E1406-35. doi: 10.1002/humu.21249.

PubMed [citation]

PMID:: 20333770

Identification of novel mutations in the ortholog of Drosophila eyes shut gene (EYS) causing autosomal recessive retinitis pigmentosa.

Abd El-Aziz MM, O'Driscoll CA, Kaye RS, Barragan I, El-Ashry MF, Borrego S, Antiñolo G, Pang CP, Webster AR, Bhattacharya SS.

Invest Ophthalmol Vis Sci. 2010 Aug;51(8):4266-72. doi: 10.1167/iovs.09-5109. Epub 2010 Mar 17. Erratum in: Invest Ophthalmol Vis Sci. 2014 Dec;55(12):8055.

PubMed [citation]

PMID:: 20237254

See all PubMed Citations (4)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq, SCV000221188.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (4)

Description

The Cys2139Tyr variant in EYS has been reported in 3 compound heterozygous and 1 heterozygous individuals with retinitis pigmentosa and was found to segregate with disease in 3 compound heterozygous family members (Audo 2010, Abd El-Aziz 2010, Jin 2014). This variant was not identified in large population studies. Computational analyses (biochemical amino acid properties, conservation, PolyPhen2, and SIFT) don't provide strong support for or against and impact to the protein and one mammal carries a tyrosine (Tyr) at this position. In summary, while segregation studies and the presence of this variant in combination with other reported pathogenic variants indicate this variant may be disease-causing, the presence of the variant amino acid in a mammal raises some concern and additional studies are required to fully establish its clinical significance.

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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000221188	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq	flagged submission Reason: Older claim that does not account for recent evidence Notes: None (LMM Criteria)	Uncertain significance (Jul 15, 2014)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20333770, 20237254, 24670872, 24033266

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000221188

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq

flagged submission

Reason: Older claim that does not account for recent evidence

Notes: None

(LMM Criteria)

Uncertain significance
(Jul 15, 2014)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Last Updated: Nov 10, 2024

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