NM_001034853.2(RPGR):c.3092del (p.Glu1031fs) AND Retinitis pigmentosa

Germline classification:: 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:: RCV001724237.5

Allele description [Variation Report for NM_001034853.2(RPGR):c.3092del (p.Glu1031fs)]

NM_001034853.2(RPGR):c.3092del (p.Glu1031fs)

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.3092del (p.Glu1031fs)

HGVS:

NC_000023.11:g.38285907del
NG_009553.1:g.46629del
NM_000328.3:c.1905+1187del
NM_001034853.2:c.3092delMANE SELECT
NM_001367245.1:c.1902+1187del
NM_001367246.1:c.1719+1187del
NM_001367247.1:c.1572+5052del
NM_001367248.1:c.1602+5052del
NM_001367249.1:c.1569+5052del
NM_001367250.1:c.1569+5052del
NM_001367251.1:c.1386+5052del
NP_001030025.1:p.Glu1031fs
NC_000023.10:g.38145160del
NC_000023.10:g.38145160del
NM_000328.3:c.1905+1187del
NM_001034853.1:c.3092del
NM_001034853.1:c.3092delA

Protein change:

E1031fs

Links:

dbSNP: rs1186795749

NCBI 1000 Genomes Browser:

rs1186795749

Molecular consequence:

NM_001034853.2:c.3092del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000328.3:c.1905+1187del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+1187del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+1187del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+5052del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+5052del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+5052del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+5052del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+5052del - 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
SCV001950366	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 1, 2021)	germline	curation	PubMed (3) [See all records that cite these PMIDs] 31645972, 25741868, 34906470

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001950366

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

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 1, 2021)

germline

curation

PubMed (3)
[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

Clinical and genetic characteristics of 14 patients from 13 Japanese families with RPGR-associated retinal disorder: report of eight novel variants.

Mawatari G, Fujinami K, Liu X, Yang L, Yokokawa YF, Komori S, Ueno S, Terasaki H, Katagiri S, Hayashi T, Kuniyoshi K, Miyake Y, Tsunoda K, Yoshitake K, Iwata T, Nao-I N; JEGC study group.

Hum Genome Var. 2019;6:34. doi: 10.1038/s41439-019-0065-7. Erratum in: Hum Genome Var. 2020 Feb 10;7:3. doi: 10.1038/s41439-019-0086-2.

PubMed [citation]

PMID:: 31645972
PMCID:: PMC6804603

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

See all PubMed Citations (3)

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001950366.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (3)

Description

The p.Glu1031GlyfsTer58 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, PP3, PM2, PP1-M. Based on this evidence we have classified this variant as 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: Nov 30, 2024

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