NM_001142800.2(EYS):c.6404_6415del (p.Thr2135_Cys2139delinsSer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 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:: RCV003567782.2

Allele description [Variation Report for NM_001142800.2(EYS):c.6404_6415del (p.Thr2135_Cys2139delinsSer)]

NM_001142800.2(EYS):c.6404_6415del (p.Thr2135_Cys2139delinsSer)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.6404_6415del (p.Thr2135_Cys2139delinsSer)

HGVS:

NC_000006.12:g.64230601_64230612del
NG_023443.2:g.1481614_1481625del
NM_001142800.2:c.6404_6415delMANE SELECT
NM_001292009.2:c.6404_6415del
NP_001136272.1:p.Thr2135_Cys2139delinsSer
NP_001278938.1:p.Thr2135_Cys2139delinsSer
NC_000006.11:g.64940494_64940505del

Molecular consequence:

NM_001142800.2:c.6404_6415del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001292009.2:c.6404_6415del - inframe_indel - [Sequence Ontology: SO:0001820]

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
SCV004324410	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 19, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20333770, 25356976, 25753737, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004324410

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 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

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

Genotype-phenotype correlation and mutation spectrum in a large cohort of patients with inherited retinal dystrophy revealed by next-generation sequencing.

Huang XF, Huang F, Wu KC, Wu J, Chen J, Pang CP, Lu F, Qu J, Jin ZB.

Genet Med. 2015 Apr;17(4):271-8. doi: 10.1038/gim.2014.138. Epub 2014 Nov 6.

PubMed [citation]

PMID:: 25356976

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004324410.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the EYS protein in which other variant(s) (p.Cys2139Tyr) have been determined to be pathogenic (PMID: 20333770, 25356976, 25753737). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with EYS-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.6404_6415del, is a complex sequence change that results in the deletion of 5 and insertion of 1 amino acid(s) in the EYS protein (p.Thr2135_Cys2139delinsSer).

#	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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