NM_001034853.2(RPGR):c.2937_2938del (p.Glu980fs) AND Retinitis pigmentosa

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 1, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001724284.3

Allele description [Variation Report for NM_001034853.2(RPGR):c.2937_2938del (p.Glu980fs)]

NM_001034853.2(RPGR):c.2937_2938del (p.Glu980fs)

Gene:

RPGR:retinitis pigmentosa GTPase regulator [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001034853.2(RPGR):c.2937_2938del (p.Glu980fs)

HGVS:

NC_000023.11:g.38286063_38286064del
NG_009553.1:g.46474_46475del
NM_000328.3:c.1905+1032_1905+1033del
NM_001034853.2:c.2937_2938delMANE SELECT
NM_001367245.1:c.1902+1032_1902+1033del
NM_001367246.1:c.1719+1032_1719+1033del
NM_001367247.1:c.1572+4897_1572+4898del
NM_001367248.1:c.1602+4897_1602+4898del
NM_001367249.1:c.1569+4897_1569+4898del
NM_001367250.1:c.1569+4897_1569+4898del
NM_001367251.1:c.1386+4897_1386+4898del
NP_001030025.1:p.Glu980fs
NC_000023.10:g.38145314_38145315del
NC_000023.10:g.38145316_38145317del
NM_001034853.1:c.2937_2938del

Protein change:

E980fs

Links:

dbSNP: rs2067138439

NCBI 1000 Genomes Browser:

rs2067138439

Molecular consequence:

NM_001034853.2:c.2937_2938del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000328.3:c.1905+1032_1905+1033del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+1032_1902+1033del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+1032_1719+1033del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+4897_1572+4898del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+4897_1602+4898del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+4897_1569+4898del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+4897_1569+4898del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+4897_1386+4898del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Retinitis pigmentosa (RP)
Synonyms:: Tapetoretinal degeneration
Identifiers:: MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001950365	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 1, 2021)	germline	curation	PubMed (2) [See all records that cite these PMIDs] 25741868, 34906470

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001950365

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 1, 2021)

germline

curation

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	curation

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

The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK).

Zampaglione E, Maher M, Place EM, Wagner NE, DiTroia S, Chao KR, England E, Cmg B, Catomeris A, Nassiri S, Himes S, Pagliarulo J, Ferguson C, Galdikaité-Braziené E, Cole B, Pierce EA, Bujakowska KM.

Genet Med. 2022 Feb;24(2):332-343. doi: 10.1016/j.gim.2021.09.015. Epub 2021 Nov 30.

PubMed [citation]

PMID:: 34906470
PMCID:: PMC9200473

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001950365.1

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

Description

The p.Glu980GlyfsTer98 variant in RPGR was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). 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. If you have any questions about the classification please reach out to the Pierce Lab.

#	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: Sep 29, 2024

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