NM_001142800.2(EYS):c.1155T>A (p.Cys385Ter) AND Retinitis pigmentosa 25

Germline classification:: Pathogenic/Likely pathogenic (6 submissions)
Last evaluated:: Sep 5, 2023
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:: RCV000664630.8

Allele description [Variation Report for NM_001142800.2(EYS):c.1155T>A (p.Cys385Ter)]

NM_001142800.2(EYS):c.1155T>A (p.Cys385Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.1155T>A (p.Cys385Ter)

HGVS:

NC_000006.12:g.65402507A>T
NG_023443.2:g.309719T>A
NM_001142800.2:c.1155T>AMANE SELECT
NM_001142801.2:c.1155T>A
NM_001292009.2:c.1155T>A
NM_198283.2:c.1155T>A
NP_001136272.1:p.Cys385Ter
NP_001136273.1:p.Cys385Ter
NP_001278938.1:p.Cys385Ter
NP_938024.1:p.Cys385Ter
NC_000006.11:g.66112400A>T
NM_001142800.1:c.1155T>A

Protein change:

C385*

Links:

dbSNP: rs143994166

NCBI 1000 Genomes Browser:

rs143994166

Molecular consequence:

NM_001142800.2:c.1155T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001142801.2:c.1155T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001292009.2:c.1155T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_198283.2:c.1155T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Retinitis pigmentosa 25 (RP25)
Synonyms:: RP 25
Identifiers:: MONDO: MONDO:0011272; MedGen: C1864446; Orphanet: 791; OMIM: 602772

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000788626	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Pathogenic (Jan 3, 2018)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 28704921, 27208204 Citation Link,
SCV001142363	Reproductive Health Research and Development, BGI Genomics	no assertion criteria provided	Pathogenic (Jan 6, 2020)	germline	curation
SCV002076680	Natera, Inc.	no assertion criteria provided	Pathogenic (Jan 28, 2021)	germline	clinical testing
SCV002761769	Genetics and Molecular Pathology, SA Pathology See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 19, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004192941	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 5, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004235288	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 23, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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, curation
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

EYS Mutations Causing Autosomal Recessive Retinitis Pigmentosa: Changes of Retinal Structure and Function with Disease Progression.

McGuigan DB, Heon E, Cideciyan AV, Ratnapriya R, Lu M, Sumaroka A, Roman AJ, Batmanabane V, Garafalo AV, Stone EM, Swaroop A, Jacobson SG.

Genes (Basel). 2017 Jul 12;8(7). doi:pii: E178. 10.3390/genes8070178.

PubMed [citation]

PMID:: 28704921
PMCID:: PMC5541311

Molecular findings from 537 individuals with inherited retinal disease.

Ellingford JM, Barton S, Bhaskar S, O'Sullivan J, Williams SG, Lamb JA, Panda B, Sergouniotis PI, Gillespie RL, Daiger SP, Hall G, Gale T, Lloyd IC, Bishop PN, Ramsden SC, Black GCM.

J Med Genet. 2016 Nov;53(11):761-767. doi: 10.1136/jmedgenet-2016-103837. Epub 2016 May 11.

PubMed [citation]

PMID:: 27208204
PMCID:: PMC5106339

See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000788626.1

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

From Reproductive Health Research and Development, BGI Genomics, SCV001142363.1

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

Description

NM_001142800.1:c.1155T>A in the EYS gene has an allele frequency of 0.006 in European (Finnish) subpopulation in the gnomAD database. The EYS c.1155T>A (p.Cys385*) variant results in a premature termination codon, predicted to cause a truncated or absent EYS protein due to nonsense mediated decay. This variant has been observed in a patient with retinitis pigmentosa, in a compound heterozygous state with c.8648_8655delCATGCAGA (p.Thr2883Lysfs*4) (PMID: 28704921). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PVS1; PM3; PP4.

#	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 Natera, Inc., SCV002076680.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genetics and Molecular Pathology, SA Pathology, SCV002761769.1

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

#	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 Baylor Genetics, SCV004192941.1

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

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

From Revvity Omics, Revvity, SCV004235288.1

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

#	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: Mar 30, 2024

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