NM_020366.4(RPGRIP1):c.3749-2A>G AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 11, 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:: RCV001226493.8

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.3749-2A>G]

NM_020366.4(RPGRIP1):c.3749-2A>G

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

14q11.2

Genomic location:

Preferred name:

NM_020366.4(RPGRIP1):c.3749-2A>G

HGVS:

NC_000014.9:g.21351102A>G
NG_008933.1:g.68126A>G
NG_008933.2:g.76021A>G
NG_009932.1:g.38165T>C
NM_001377523.1:c.1727-2A>G
NM_001377948.1:c.2675-2A>G
NM_001377949.1:c.1835-2A>G
NM_001377950.1:c.1727-2A>G
NM_001377951.1:c.1232-2A>G
NM_020366.4:c.3749-2A>GMANE SELECT
NC_000014.8:g.21819261A>G
NM_020366.3:c.3749-2A>G

Links:

dbSNP: rs376517859

NCBI 1000 Genomes Browser:

rs376517859

Molecular consequence:

NM_001377523.1:c.1727-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001377948.1:c.2675-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001377949.1:c.1835-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001377950.1:c.1727-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001377951.1:c.1232-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_020366.4:c.3749-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

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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GPD2 [Papio anubis]
GPD2 [Papio anubis]
Gene ID:101002517

Gene
HS3ST6 [Papio anubis]
HS3ST6 [Papio anubis]
Gene ID:101020207

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001398808	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 11, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23847139, 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001398808

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 11, 2023)

germline

clinical testing

PubMed (4)
[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

Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing.

Wang X, Wang H, Sun V, Tuan HF, Keser V, Wang K, Ren H, Lopez I, Zaneveld JE, Siddiqui S, Bowles S, Khan A, Salvo J, Jacobson SG, Iannaccone A, Wang F, Birch D, Heckenlively JR, Fishman GA, Traboulsi EI, Li Y, Wheaton D, et al.

J Med Genet. 2013 Oct;50(10):674-88. doi: 10.1136/jmedgenet-2013-101558. Epub 2013 Jul 11.

PubMed [citation]

PMID:: 23847139
PMCID:: PMC3932025

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001398808.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change affects an acceptor splice site in intron 23 of the RPGRIP1 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is present in population databases (rs376517859, gnomAD 0.01%). Disruption of this splice site has been observed in individual(s) with Leber congenital amaurosis (PMID: 23847139). ClinVar contains an entry for this variant (Variation ID: 195835). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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