NM_001142800.2(EYS):c.8834G>A (p.Gly2945Glu) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 25, 2023
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:: RCV001037096.5

Allele description [Variation Report for NM_001142800.2(EYS):c.8834G>A (p.Gly2945Glu)]

NM_001142800.2(EYS):c.8834G>A (p.Gly2945Glu)

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.8834G>A (p.Gly2945Glu)

HGVS:

NC_000006.12:g.63721197C>T
NG_023443.2:g.1991029G>A
NG_034034.2:g.90397C>T
NM_001142800.2:c.8834G>AMANE SELECT
NM_001290259.2:c.*7489C>T
NM_001292009.2:c.8897G>A
NM_001370348.2:c.*7489C>TMANE SELECT
NM_001370349.2:c.*7489C>T
NM_001370350.2:c.*7489C>T
NM_015153.4:c.*7489C>T
NP_001136272.1:p.Gly2945Glu
NP_001278938.1:p.Gly2966Glu
NC_000006.11:g.64431093C>T
NC_000006.11:g.64431093C>T
NM_001142800.1:c.8834G>A

Protein change:

G2945E

Links:

dbSNP: rs1161453292

NCBI 1000 Genomes Browser:

rs1161453292

Molecular consequence:

NM_001290259.2:c.*7489C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370348.2:c.*7489C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370349.2:c.*7489C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370350.2:c.*7489C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_015153.4:c.*7489C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001142800.2:c.8834G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001292009.2:c.8897G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001200493	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 25, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 21069908, 21519034, 32036094, 32728228, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001200493

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 25, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

Citations

PubMed

Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa.

Barragán I, Borrego S, Pieras JI, González-del Pozo M, Santoyo J, Ayuso C, Baiget M, Millan JM, Mena M, Abd El-Aziz MM, Audo I, Zeitz C, Littink KW, Dopazo J, Bhattacharya SS, Antiñolo G.

Hum Mutat. 2010 Nov;31(11):E1772-800.

PubMed [citation]

PMID:: 21069908
PMCID:: PMC3045506

Copy-number variations in EYS: a significant event in the appearance of arRP.

Pieras JI, Barragán I, Borrego S, Audo I, González-Del Pozo M, Bernal S, Baiget M, Zeitz C, Bhattacharya SS, Antiñolo G.

Invest Ophthalmol Vis Sci. 2011 Jul 29;52(8):5625-31. doi: 10.1167/iovs.11-7292.

PubMed [citation]

PMID:: 21519034

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001200493.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 2945 of the EYS protein (p.Gly2945Glu). This variant is present in population databases (no rsID available, gnomAD 0.004%). This missense change has been observed in individuals with retinitis pigmentosa (PMID: 21069908, 21519034, 32036094, 32728228; Invitae). It has also been observed to segregate with disease in related individuals. This variant is also known as Gly2966Glu. ClinVar contains an entry for this variant (Variation ID: 836062). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on EYS protein function. For these reasons, this variant has been 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: Sep 29, 2024

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