NM_001142800.2(EYS):c.5834_5835+4del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 19, 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:: RCV000813522.8

Allele description [Variation Report for NM_001142800.2(EYS):c.5834_5835+4del]

NM_001142800.2(EYS):c.5834_5835+4del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.5834_5835+4del

HGVS:

NC_000006.11:g.65149051_65149056del
NC_000006.12:g.64439161_64439166del
NG_023443.2:g.1273063_1273068del
NM_001142800.2:c.5834_5835+4delMANE SELECT
NM_001292009.2:c.5834_5835+4del
NC_000006.11:g.65149051_65149056del
NC_000006.11:g.65149051_65149056delTTACCT
NC_000006.11:g.65149054_65149059del
NM_001142800.1:c.5834_5835+4del
NM_001142800.1:c.5834_5835+4delAGGTAA

Links:

dbSNP: rs1582753394

NCBI 1000 Genomes Browser:

rs1582753394

Molecular consequence:

NM_001142800.2:c.5834_5835+4del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001292009.2:c.5834_5835+4del - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV000953884	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 19, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 18836446, 20333770, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000953884

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 19, 2023)

germline

clinical testing

PubMed (4)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa.

Abd El-Aziz MM, Barragan I, O'Driscoll CA, Goodstadt L, Prigmore E, Borrego S, Mena M, Pieras JI, El-Ashry MF, Safieh LA, Shah A, Cheetham ME, Carter NP, Chakarova C, Ponting CP, Bhattacharya SS, Antinolo G.

Nat Genet. 2008 Nov;40(11):1285-7. doi: 10.1038/ng.241. Epub 2008 Oct 5.

PubMed [citation]

PMID:: 18836446
PMCID:: PMC2719291

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000953884.6

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

Description

This variant results in the deletion of part of exon 27 (c.5834_5835+4del) of the EYS gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EYS are known to be pathogenic (PMID: 18836446, 20333770). This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with EYS-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 656986). 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 20, 2024

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