NM_000330.3(RS1):c.579del (p.Ile194fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Sep 4, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000058880.3

Allele description [Variation Report for NM_000330.3(RS1):c.579del (p.Ile194fs)]

NM_000330.3(RS1):c.579del (p.Ile194fs)

Genes:
CDKL5:cyclin dependent kinase like 5 [Gene - OMIM - HGNC]
RS1:retinoschisin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp22.13
Genomic location:
Preferred name:
NM_000330.3(RS1):c.579del (p.Ile194fs)
HGVS:
  • NC_000023.11:g.18642105del
  • NG_008475.1:g.221501del
  • NG_008659.3:g.40349del
  • NM_000330.3:c.579del
  • NM_001037343.1:c.2714-3902del
  • NM_003159.2:c.2714-3902del
  • NP_000321.1:p.Ile194fs
  • LRG_702t1:c.579del
  • LRG_702:g.40349del
  • LRG_702p1:p.Ile194fs
  • NC_000023.10:g.18660220del
  • NC_000023.10:g.18660225del
  • NM_000330.3:c.579delC
Protein change:
I194fs
Links:
dbSNP: rs199469697
NCBI 1000 Genomes Browser:
rs199469697
Molecular consequence:
  • NM_000330.3:c.579del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001037343.1:c.2714-3902del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003159.2:c.2714-3902del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000090400SN ONGC Dept of Genetics and Molecular biology Vision Research Foundationno assertion criteria providedunknowngermlinenot provided

SCV001372557Invitaecriteria provided, single submitter
Pathogenic
(Sep 4, 2019)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Description

central and peripheral schisis

SCV000090400

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot provided1not providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genotypic and phenotypic spectrum of X-linked retinoschisis in Australia.

Hewitt AW, FitzGerald LM, Scotter LW, Mulhall LE, McKay JD, Mackey DA.

Clin Exp Ophthalmol. 2005 Jun;33(3):233-9.

PubMed [citation]
PMID:
15932525

[Detection and prenatal diagnosis for RS1 gene mutations in two Chinese families with X-linked juvenile retinoschisis].

Chu Y, Fang D, Hou QF, Wang LY, Guo XR, Wang YT, Liao SX.

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2013 Apr;30(2):199-202. doi: 10.3760/cma.j.issn.1003-9406.2013.04.017. Chinese.

PubMed [citation]
PMID:
23568735
See all PubMed Citations (4)

Details of each submission

From SN ONGC Dept of Genetics and Molecular biology Vision Research Foundation, SCV000090400.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided

Description

Converted during submission to Uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot provided1not providednot providednot providednot providednot providednot provided

From Invitae, SCV001372557.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change results in a frameshift in the RS1 gene (p.Ile194Serfs*43). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 31 amino acids of the RS1 protein and extend the protein by an additional 11 amino acids. This variant is not present in population databases (ExAC no frequency). This protein extension has been observed in individuals affected with X-linked retinoschisis (PMID: 29851975, 15932525, 23568735, Invitae). ClinVar contains an entry for this variant (Variation ID: 68076). This variant has been reported to affect RS1 protein function (PMID: 29851975). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 24, 2021

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