NM_001142800.2(EYS):c.4350_4356del (p.Ile1451fs) AND not provided

Germline classification:: Pathogenic (6 submissions)
Last evaluated:: Jan 7, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000723898.37

Allele description [Variation Report for NM_001142800.2(EYS):c.4350_4356del (p.Ile1451fs)]

NM_001142800.2(EYS):c.4350_4356del (p.Ile1451fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.4350_4356del (p.Ile1451fs)

HGVS:

NC_000006.12:g.64591514_64591520del
NG_023443.2:g.1120709_1120715del
NM_001142800.2:c.4350_4356delMANE SELECT
NM_001292009.2:c.4350_4356del
NP_001136272.1:p.Ile1451fs
NP_001278938.1:p.Ile1451fs
NC_000006.11:g.65301404_65301410del
NC_000006.11:g.65301407_65301413del
NM_001142800.1:c.4350_4356delTATAGCT
NM_001142800.2:c.4350_4356delTATAGCTMANE SELECT
NM_001292009.1:c.4350_4356delTATAGCT

Protein change:

I1451fs

Links:

dbSNP: rs761238771

NCBI 1000 Genomes Browser:

rs761238771

Molecular consequence:

NM_001142800.2:c.4350_4356del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001292009.2:c.4350_4356del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Gene ID:71041410

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000228311	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Jun 24, 2014)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20537394, 21217109 Citation Link,
SCV001168538	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Oct 7, 2022)	germline	clinical testing	Citation Link,
SCV001218945	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 7, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 18836446, 20333770, 20537394, 24265693, 31074760, 28492532
SCV001248826	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jul 1, 2020)	germline	clinical testing	Citation Link,
SCV001921019	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001956061	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	6	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

High-resolution homozygosity mapping is a powerful tool to detect novel mutations causative of autosomal recessive RP in the Dutch population.

Collin RW, van den Born LI, Klevering BJ, de Castro-Miró M, Littink KW, Arimadyo K, Azam M, Yazar V, Zonneveld MN, Paun CC, Siemiatkowska AM, Strom TM, Hehir-Kwa JY, Kroes HY, de Faber JT, van Schooneveld MJ, Heckenlively JR, Hoyng CB, den Hollander AI, Cremers FP.

Invest Ophthalmol Vis Sci. 2011 Apr 6;52(5):2227-39. doi: 10.1167/iovs.10-6185.

PubMed [citation]

PMID:: 21217109

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 (7)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000228311.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

#	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		1	not provided	not provided	not provided

From GeneDx, SCV001168538.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25491159, 32531858, 21217109, 31074760, 30718709, 32037395, 20537394)

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

From Invitae, SCV001218945.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change creates a premature translational stop signal (p.Ile1451Profs*3) in the EYS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EYS are known to be pathogenic (PMID: 18836446, 20333770). This variant is present in population databases (rs761238771, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with autosomal recessive retinitis pigmentosa (PMID: 20537394, 24265693, 31074760). ClinVar contains an entry for this variant (Variation ID: 195936). 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

From CeGaT Center for Human Genetics Tuebingen, SCV001248826.22

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		6	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001921019.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001956061.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

Last Updated: Jun 23, 2024

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