NM_001142800.2(EYS):c.9405T>A (p.Tyr3135Ter) AND Retinitis pigmentosa 25

Germline classification:: Pathogenic/Likely pathogenic (6 submissions)
Last evaluated:: Mar 9, 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:: RCV000000568.20

Allele description [Variation Report for NM_001142800.2(EYS):c.9405T>A (p.Tyr3135Ter)]

NM_001142800.2(EYS):c.9405T>A (p.Tyr3135Ter)

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.9405T>A (p.Tyr3135Ter)

HGVS:

NC_000006.12:g.63720626A>T
NG_023443.2:g.1991600T>A
NG_034034.2:g.89826A>T
NM_001142800.2:c.9405T>AMANE SELECT
NM_001290259.2:c.*6918A>T
NM_001292009.2:c.9468T>A
NM_001370348.2:c.*6918A>TMANE SELECT
NM_001370349.2:c.*6918A>T
NM_001370350.2:c.*6918A>T
NM_015153.4:c.*6918A>T
NP_001136272.1:p.Tyr3135Ter
NP_001278938.1:p.Tyr3156Ter
NC_000006.11:g.64430522A>T
NM_001142800.1:c.9405T>A

Protein change:

Y3135*; TYR3156TER

Links:

OMIM: 612424.0005; dbSNP: rs137853190

NCBI 1000 Genomes Browser:

rs137853190

Molecular consequence:

NM_001290259.2:c.*6918A>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370348.2:c.*6918A>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370349.2:c.*6918A>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370350.2:c.*6918A>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_015153.4:c.*6918A>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001142800.2:c.9405T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001292009.2:c.9468T>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
SCV000020717	OMIM	no assertion criteria provided	Pathogenic (Nov 1, 2008)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000796512	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Dec 19, 2017)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18976725, 21069908 Citation Link,
SCV000894389	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 31, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002024538	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 11, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002519620	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link,
SCV004192853	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 9, 2024)	unknown	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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of a 2 Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa.

Collin RW, Littink KW, Klevering BJ, van den Born LI, Koenekoop RK, Zonneveld MN, Blokland EA, Strom TM, Hoyng CB, den Hollander AI, Cremers FP.

Am J Hum Genet. 2008 Nov;83(5):594-603. doi: 10.1016/j.ajhg.2008.10.014. Epub 2008 Oct 30.

PubMed [citation]

PMID:: 18976725
PMCID:: PMC2668042

Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa.

Barragán I, Borrego S, Pieras JI, González-del Pozo M, Santoyo J, Ayuso C, Baiget M, Millan JM, Mena M, Abd El-Aziz MM, Audo I, Zeitz C, Littink KW, Dopazo J, Bhattacharya SS, Antiñolo G.

Hum Mutat. 2010 Nov;31(11):E1772-800.

PubMed [citation]

PMID:: 21069908
PMCID:: PMC3045506

See all PubMed Citations (3)

PMC

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.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]

PMCID:: PMC4544753
PMID:: 25741868
DOI:: 10.1038/gim.2015.30

Details of each submission

From OMIM, SCV000020717.2

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

Description

In 2 sibs with autosomal recessive retinitis pigmentosa (RP25; 602772), Collin et al. (2008) identified homozygosity for a 9468T-A transversion in exon 44 of the EYS gene, predicted to cause a tyr3156-to-ter (Y3156X) substitution resulting in truncation of the 10 C-terminal amino acids of the protein, some of which are well conserved. The authors subsequently conducted allele-specific PCR in 131 unrelated RP patients and identified the Y3156X mutation in another proband and her 2 affected sibs. Microsatellite and SNP analysis revealed that Y3156X was present on the same haplotype in both families, suggesting a founder effect. The mutation was either absent or present in heterozygosity in unaffected family members, and was not found in 552 alleles from ethnically matched controls.

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

From Counsyl, SCV000796512.1

#	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 Fulgent Genetics, Fulgent Genetics, SCV000894389.1

#	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, SCV002024538.3

#	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

From Mendelics, SCV002519620.1

#	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 Baylor Genetics, SCV004192853.2

#	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: Sep 29, 2024

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