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NM_019098.5(CNGB3):c.644-1G>C

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 1, 2021)
Last evaluated:
Oct 2, 2020
Accession:
VCV000188780.10
Variation ID:
188780
Description:
single nucleotide variant
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NM_019098.5(CNGB3):c.644-1G>C

Allele ID
186769
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q21.3
Genomic location
8: 86667134 (GRCh38) GRCh38 UCSC
8: 87679362 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.87679362C>G
NM_019098.4:c.644-1G>C splice acceptor
NC_000008.11:g.86667134C>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000008.11:86667133:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00004
The Genome Aggregation Database (gnomAD) 0.00006
The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00003
Links
ClinGen: CA273948
dbSNP: rs201794629
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Oct 2, 2020 RCV000814009.6
Likely pathogenic 2 criteria provided, single submitter May 12, 2014 RCV000169108.2
Pathogenic 2 no assertion criteria provided Sep 16, 2020 RCV001002980.2
not provided 1 no assertion provided - RCV001535671.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CNGB3 - - GRCh38
GRCh37
561 590

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(May 12, 2014)
criteria provided, single submitter
Method: literature only
Achromatopsia 3
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220308.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (1)
Pathogenic
(Oct 02, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000954397.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects an acceptor splice site in intron 5 of the CNGB3 gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Jan 06, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001819278.1
Submitted: (Sep 01, 2021)
Evidence details
Comment:
Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: … (more)
Pathogenic
(Jun 23, 2019)
no assertion criteria provided
Method: research
achromatopsia
Allele origin: inherited
Sharon lab,Hadassah-Hebrew University Medical Center
Accession: SCV001161033.1
Submitted: (Jun 25, 2019)
Evidence details
Pathogenic
(Mar 27, 2017)
no assertion criteria provided
Method: research
ACHM3
Allele origin: germline
Molecular Genetics Laboratory,Institute for Ophthalmic Research
Accession: SCV000575843.1
Submitted: (Apr 06, 2017)
Evidence details
Publications
PubMed (1)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Achromatopsia
Allele origin: germline
Natera, Inc.
Accession: SCV001454554.1
Submitted: (Dec 28, 2020)
Evidence details
not provided
(-)
no assertion provided
Method: phenotyping only
Achromatopsia 3
Stargardt disease 1
Retinitis pigmentosa
Allele origin: unknown
GenomeConnect - Invitae Patient Insights Network
Accession: SCV001749734.1
Submitted: (Apr 26, 2021)
Evidence details
Comment:
Variant interpreted as Pathogenic and reported on 02-21-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
CNGB3 mutation spectrum including copy number variations in 552 achromatopsia patients. Mayer AK Human mutation 2017 PMID: 28795510
Genetics and Disease Expression in the CNGA3 Form of Achromatopsia: Steps on the Path to Gene Therapy. Zelinger L Ophthalmology 2015 PMID: 25616768
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
CNGB3 mutations account for 50% of all cases with autosomal recessive achromatopsia. Kohl S European journal of human genetics : EJHG 2005 PMID: 15657609

Text-mined citations for rs201794629...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021