U.S. flag

An official website of the United States government

NM_001297.5(CNGB1):c.3560G>A (p.Arg1187Gln) AND not provided

Germline classification:
Benign (4 submissions)
Last evaluated:
Dec 3, 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:
RCV001358311.10

Allele description [Variation Report for NM_001297.5(CNGB1):c.3560G>A (p.Arg1187Gln)]

NM_001297.5(CNGB1):c.3560G>A (p.Arg1187Gln)

Gene:
CNGB1:cyclic nucleotide gated channel subunit beta 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q21
Genomic location:
Preferred name:
NM_001297.5(CNGB1):c.3560G>A (p.Arg1187Gln)
HGVS:
  • NC_000016.10:g.57884360C>T
  • NG_016351.1:g.91757G>A
  • NM_001286130.2:c.3542G>A
  • NM_001297.5:c.3560G>AMANE SELECT
  • NP_001273059.1:p.Arg1181Gln
  • NP_001288.3:p.Arg1187Gln
  • NC_000016.9:g.57918264C>T
  • NM_001297.4:c.3560G>A
Protein change:
R1181Q
Links:
dbSNP: rs543712958
NCBI 1000 Genomes Browser:
rs543712958
Molecular consequence:
  • NM_001286130.2:c.3542G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001297.5:c.3560G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001554011Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

SCV001725236Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Dec 3, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001918140Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Likely benigngermlineclinical testing

SCV001965613Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Likely benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001554011.1

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

Description

The CNGB1 p.Arg1181Gln variant was not identified in the literature but was identified in dbSNP (ID: rs543712958), ClinVar (classified as uncertain significance by Illumina) and LOVD 3.0 (classified as likely benign). The variant was identified in control databases in 276 of 269178 chromosomes (1 homozygous) at a frequency of 0.001025 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 253 of 30428 chromosomes (freq: 0.008315), Other in 2 of 6942 chromosomes (freq: 0.000288), European (non-Finnish) in 19 of 120534 chromosomes (freq: 0.000158) and African in 2 of 22564 chromosomes (freq: 0.000089), but was not observed in the Latino, Ashkenazi Jewish, East Asian, or European (Finnish) populations. The p.Arg1181 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and three of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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

From Invitae, SCV001725236.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001918140.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001965613.1

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

Last Updated: May 26, 2024