NM_020366.4(RPGRIP1):c.1087_1090del (p.Arg363fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 19, 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:: RCV003781400.2

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.1087_1090del (p.Arg363fs)]

NM_020366.4(RPGRIP1):c.1087_1090del (p.Arg363fs)

Gene:

RPGRIP1:RPGR interacting protein 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

14q11.2

Genomic location:

Preferred name:

NM_020366.4(RPGRIP1):c.1087_1090del (p.Arg363fs)

HGVS:

NC_000014.9:g.21312440AG[1]
NG_008933.1:g.29464AG[1]
NG_008933.2:g.37359AG[1]
NM_020366.4:c.1087_1090delMANE SELECT
NP_065099.3:p.Arg363fs
NC_000014.8:g.21780598_21780601del
NC_000014.8:g.21780599AG[1]

Protein change:

R363fs

Molecular consequence:

NM_020366.4:c.1087_1090del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Cone-rod dystrophy 13 (CORD13)
Identifiers:: MONDO: MONDO:0011987; MedGen: C2750720; Orphanet: 1872; OMIM: 608194

Name:: Leber congenital amaurosis 6 (LCA6)
Identifiers:: MONDO: MONDO:0013446; MedGen: C1854260; Orphanet: 65; OMIM: 613826

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004573390	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 19, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 29343940, 30072743, 11528500, 23105016, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004573390

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 19, 2023)

germline

clinical testing

PubMed (5)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Prescreening whole exome sequencing results from patients with retinal degeneration for variants in genes associated with retinal degeneration.

Bryant L, Lozynska O, Maguire AM, Aleman TS, Bennett J.

Clin Ophthalmol. 2018;12:49-63. doi: 10.2147/OPTH.S147684.

PubMed [citation]

PMID:: 29343940
PMCID:: PMC5749571

Contribution of noncoding pathogenic variants to RPGRIP1-mediated inherited retinal degeneration.

Jamshidi F, Place EM, Mehrotra S, Navarro-Gomez D, Maher M, Branham KE, Valkanas E, Cherry TJ, Lek M, MacArthur D, Pierce EA, Bujakowska KM.

Genet Med. 2019 Mar;21(3):694-704. doi: 10.1038/s41436-018-0104-7. Epub 2018 Aug 3.

PubMed [citation]

PMID:: 30072743
PMCID:: PMC6399075

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004573390.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This premature translational stop signal has been observed in individual(s) with clinical features of RPGRIP1-related conditions (PMID: 29343940, 30072743). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant is also known as c.1084_1087del, p.E362NAfs*12. This variant is present in population databases (rs768719934, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Arg363Leufs*11) in the RPGRIP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RPGRIP1 are known to be pathogenic (PMID: 11528500, 23105016).

#	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: Sep 29, 2024

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