NM_001034853.2(RPGR):c.2567_2568del (p.Gly856fs) AND Retinitis pigmentosa

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 24, 2023
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:: RCV003324677.2

Allele description [Variation Report for NM_001034853.2(RPGR):c.2567_2568del (p.Gly856fs)]

NM_001034853.2(RPGR):c.2567_2568del (p.Gly856fs)

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.2567_2568del (p.Gly856fs)

Other names:

NC_000023.10:g.38145685_38145686del; NP_001030025.1:p.(Gly856GlufsTer222)

HGVS:

NC_000023.11:g.38286432_38286433del
NG_009553.1:g.46104_46105del
NM_000328.3:c.1905+662_1905+663del
NM_001034853.2:c.2567_2568delMANE SELECT
NM_001367245.1:c.1902+662_1902+663del
NM_001367246.1:c.1719+662_1719+663del
NM_001367247.1:c.1572+4527_1572+4528del
NM_001367248.1:c.1602+4527_1602+4528del
NM_001367249.1:c.1569+4527_1569+4528del
NM_001367250.1:c.1569+4527_1569+4528del
NM_001367251.1:c.1386+4527_1386+4528del
NP_001030025.1:p.Gly856fs
NC_000023.10:g.38145685_38145686del
NM_001034853.1:c.2567_2568del

Protein change:

G856fs

Molecular consequence:

NM_001034853.2:c.2567_2568del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000328.3:c.1905+662_1905+663del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+662_1902+663del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+662_1719+663del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+4527_1572+4528del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+4527_1602+4528del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+4527_1569+4528del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+4527_1569+4528del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+4527_1386+4528del - 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

Recent activity

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NADH dehydrogenase subunit 6 (mitochondrion) [Meretrix petechialis]
NADH dehydrogenase subunit 6 (mitochondrion) [Meretrix petechialis]
gi|238908492|ref|YP_002929384.1|

Protein
NADH dehydrogenase subunit 6 (mitochondrion) [Argopecten irradians]
NADH dehydrogenase subunit 6 (mitochondrion) [Argopecten irradians]
gi|153123679|gnl|NCBI_MITO|ND6_2124 |YP_001382290.1|

Protein
hypothetical protein P677_0897 [Acinetobacter baumannii UH7707]
hypothetical protein P677_0897 [Acinetobacter baumannii UH7707]
gi|571738190|gb|ETR26076.1||gnl|WGS |P677_0897

Protein
N-acylglucosamine 2-epimerase [Pseudonaja textilis]
N-acylglucosamine 2-epimerase [Pseudonaja textilis]
gi|1488374138|ref|XP_026567196.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004030312	Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 24, 2023)	germline	research	PubMed (2) [See all records that cite these PMIDs] 36909829, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004030312

Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jul 24, 2023)

germline

research

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	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis.

Peter VG, Kaminska K, Santos C, Quinodoz M, Cancellieri F, Cisarova K, Pescini Gobert R, Rodrigues R, Custódio S, Paris LP, Sousa AB, Coutinho Santos L, Rivolta C.

PNAS Nexus. 2023 Mar;2(3):pgad043. doi: 10.1093/pnasnexus/pgad043.

PubMed [citation]

PMID:: 36909829
PMCID:: PMC10003751

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 Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel, SCV004030312.1

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

Description

Clinical significance based on ACMG v2.0

#	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

Last Updated: May 7, 2024

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