NM_019098.5(CNGB3):c.1579-1G>A AND not provided

Clinical significance:Pathogenic (Last evaluated: Sep 3, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001092878.4

Allele description [Variation Report for NM_019098.5(CNGB3):c.1579-1G>A]

NM_019098.5(CNGB3):c.1579-1G>A

Gene:
CNGB3:cyclic nucleotide gated channel subunit beta 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q21.3
Genomic location:
Preferred name:
NM_019098.5(CNGB3):c.1579-1G>A
HGVS:
  • NC_000008.11:g.86611672C>T
  • NG_016980.1:g.137004G>A
  • NM_019098.5:c.1579-1G>AMANE SELECT
  • NC_000008.10:g.87623900C>T
  • NM_019098.4:c.1579-1G>A
Links:
dbSNP: rs1057516504
NCBI 1000 Genomes Browser:
rs1057516504
Molecular consequence:
  • NM_019098.5:c.1579-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001249601CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Pathogenic
(Dec 1, 2018)
germlineclinical testing

Citation Link,

SCV001375525Invitaecriteria provided, single submitter
Pathogenic
(Sep 3, 2019)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Five novel CNGB3 gene mutations in Polish patients with achromatopsia.

Wawrocka A, Kohl S, Baumann B, Walczak-Sztulpa J, Wicher K, Skorczyk-Werner A, Krawczynski MR.

Mol Vis. 2014;20:1732-9.

PubMed [citation]
PMID:
25558176
PMCID:
PMC4279706

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (4)

Details of each submission

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001249601.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV001375525.2

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

Description

This sequence change affects an acceptor splice site in intron 13 of the CNGB3 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with achromatopsia (PMID: 25558176, 28795510). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 370459). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CNGB3 are known to be pathogenic (PMID: 28795510). 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: Dec 4, 2021

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