NM_001142800.2(EYS):c.8606C>G (p.Ser2869Ter) AND Retinitis pigmentosa 25

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Feb 28, 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:: RCV001376254.4

Allele description [Variation Report for NM_001142800.2(EYS):c.8606C>G (p.Ser2869Ter)]

NM_001142800.2(EYS):c.8606C>G (p.Ser2869Ter)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

6q12

Genomic location:

Preferred name:

NM_001142800.2(EYS):c.8606C>G (p.Ser2869Ter)

HGVS:

NC_000006.12:g.63721425G>C
NG_023443.2:g.1990801C>G
NM_001142800.2:c.8606C>GMANE SELECT
NM_001290259.2:c.*7717G>C
NM_001292009.2:c.8669C>G
NM_001370348.2:c.*7717G>CMANE SELECT
NM_001370349.2:c.*7717G>C
NM_001370350.2:c.*7717G>C
NM_015153.4:c.*7717G>C
NP_001136272.1:p.Ser2869Ter
NP_001278938.1:p.Ser2890Ter
NC_000006.11:g.64431321G>C
NM_001142800.1:c.8606C>G

Protein change:

S2869*

Links:

dbSNP: rs933169926

NCBI 1000 Genomes Browser:

rs933169926

Molecular consequence:

NM_001290259.2:c.*7717G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370348.2:c.*7717G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370349.2:c.*7717G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370350.2:c.*7717G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_015153.4:c.*7717G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001142800.2:c.8606C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001292009.2:c.8669C>G - nonsense - [Sequence Ontology: SO:0001587]

Observations:

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
SCV001573332	Ocular Genomics Institute, Massachusetts Eye and Ear	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 8, 2021)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV001737143	DBGen Ocular Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 21, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004193498	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 28, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001573332

Ocular Genomics Institute, Massachusetts Eye and Ear

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 8, 2021)

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV001737143

DBGen Ocular Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 21, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004193498

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 28, 2024)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001573332.1

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

Description

The EYS c.8606C>G variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2. Based on this evidence we have classified this variant as Likely Pathogenic.

#	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 DBGen Ocular Genomics, SCV001737143.1

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

From Baylor Genetics, SCV004193498.2

#	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

Last Updated: Jun 17, 2024

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