NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter) AND Retinitis pigmentosa 25

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Mar 26, 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:: RCV001808400.6

Allele description [Variation Report for NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter)]

NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter)

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.8805C>A (p.Tyr2935Ter)

HGVS:

NC_000006.12:g.63721226G>T
NG_023443.2:g.1991000C>A
NG_034034.2:g.90426G>T
NM_001142800.2:c.8805C>AMANE SELECT
NM_001290259.2:c.*7518G>T
NM_001292009.2:c.8868C>A
NM_001370348.2:c.*7518G>TMANE SELECT
NM_001370349.2:c.*7518G>T
NM_001370350.2:c.*7518G>T
NM_015153.4:c.*7518G>T
NP_001136272.1:p.Tyr2935Ter
NP_001278938.1:p.Tyr2956Ter
NC_000006.11:g.64431122G>T
NM_001142800.1:c.8805C>A

Protein change:

Y2935*

Links:

dbSNP: rs527236067

NCBI 1000 Genomes Browser:

rs527236067

Molecular consequence:

NM_001290259.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370348.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370349.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001370350.2:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_015153.4:c.*7518G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001142800.2:c.8805C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001292009.2:c.8868C>A - 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
SCV002058676	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] PMID:22363543,
SCV002519629	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link,
SCV004192874	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 26, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004235278	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 19, 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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

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 3billion, SCV002058676.1

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

Description

Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region (PVS1_S). The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000143115, PMID:22363543).It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000037, PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

From Mendelics, SCV002519629.1

#	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, SCV004192874.2

#	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

From Revvity Omics, Revvity, SCV004235278.1

#	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: Oct 13, 2024

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