NM_001142800.2(EYS):c.8629_8633del (p.Thr2877fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 1, 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:: RCV003721129.1

Allele description [Variation Report for NM_001142800.2(EYS):c.8629_8633del (p.Thr2877fs)]

NM_001142800.2(EYS):c.8629_8633del (p.Thr2877fs)

Genes:

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

Variant type:

Deletion

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.8629_8633del (p.Thr2877fs)

HGVS:

NC_000006.12:g.63721398_63721402del
NG_023443.2:g.1990824_1990828del
NG_034034.2:g.90598_90602del
NM_001142800.2:c.8629_8633delMANE SELECT
NM_001290259.2:c.*7690_*7694del
NM_001292009.2:c.8692_8696del
NM_001370348.2:c.*7690_*7694delMANE SELECT
NM_001370349.2:c.*7690_*7694del
NM_001370350.2:c.*7690_*7694del
NM_015153.4:c.*7690_*7694del
NP_001136272.1:p.Thr2877fs
NP_001278938.1:p.Thr2898fs
NC_000006.11:g.64431294_64431298del

Protein change:

T2877fs

Molecular consequence:

NM_001290259.2:c.*7690_*7694del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370348.2:c.*7690_*7694del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370349.2:c.*7690_*7694del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370350.2:c.*7690_*7694del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_015153.4:c.*7690_*7694del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001142800.2:c.8629_8633del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001292009.2:c.8692_8696del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004502168	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 1, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 18976725, 29159838, 30337596, 31074760, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004502168

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 1, 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

Identification of a 2 Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa.

Collin RW, Littink KW, Klevering BJ, van den Born LI, Koenekoop RK, Zonneveld MN, Blokland EA, Strom TM, Hoyng CB, den Hollander AI, Cremers FP.

Am J Hum Genet. 2008 Nov;83(5):594-603. doi: 10.1016/j.ajhg.2008.10.014. Epub 2008 Oct 30.

PubMed [citation]

PMID:: 18976725
PMCID:: PMC2668042

EYS mutation update: In silico assessment of 271 reported and 26 novel variants in patients with retinitis pigmentosa.

Messchaert M, Haer-Wigman L, Khan MI, Cremers FPM, Collin RWJ.

Hum Mutat. 2018 Feb;39(2):177-186. doi: 10.1002/humu.23371. Epub 2017 Dec 26.

PubMed [citation]

PMID:: 29159838

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV004502168.1

#	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 creates a premature translational stop signal (p.Thr2877Leufs*11) in the EYS gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 268 amino acid(s) of the EYS protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EYS-related conditions. This variant disrupts a region of the EYS protein in which other variant(s) (p.Tyr3135*) have been determined to be pathogenic (PMID: 18976725, 29159838, 30337596, 31074760). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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: Feb 28, 2024

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