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NM_001298.3(CNGA3):c.1618G>A (p.Val540Ile) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Jan 31, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000488165.35

Allele description [Variation Report for NM_001298.3(CNGA3):c.1618G>A (p.Val540Ile)]

NM_001298.3(CNGA3):c.1618G>A (p.Val540Ile)

Gene:
CNGA3:cyclic nucleotide gated channel subunit alpha 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q11.2
Genomic location:
Preferred name:
NM_001298.3(CNGA3):c.1618G>A (p.Val540Ile)
HGVS:
  • NC_000002.12:g.98396788G>A
  • NG_009097.1:g.55634G>A
  • NM_001079878.2:c.1564G>A
  • NM_001298.3:c.1618G>AMANE SELECT
  • NP_001073347.1:p.Val522Ile
  • NP_001289.1:p.Val540Ile
  • NP_001289.1:p.Val540Ile
  • NC_000002.11:g.99013251G>A
  • NM_001298.2:c.1618G>A
Protein change:
V522I
Links:
dbSNP: rs116448158
NCBI 1000 Genomes Browser:
rs116448158
Molecular consequence:
  • NM_001079878.2:c.1564G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001298.3:c.1618G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
5

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000575230CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(Aug 1, 2019)
germlineclinical testing

Citation Link,

SCV000702408Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Uncertain significance
(Nov 8, 2016)
germlineclinical testing

Citation Link,

SCV001657888Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 31, 2024)
germlineclinical testing

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

SCV001820290GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Mar 8, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing
not providedgermlineunknown2not 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 CeGaT Center for Human Genetics Tuebingen, SCV000575230.29

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

From Eurofins Ntd Llc (ga), SCV000702408.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

From Invitae, SCV001657888.4

#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 GeneDx, SCV001820290.1

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Observed in apparent homozygous state in patients with CNGA3-related retinal dystrophies in published literature (Sun et al., 2020); Observed as a single heterozygous variant in individuals with retinal dystrophies including achromatopsia in published literature, however, a second CNGA3 variant was not identified in these individuals and some had additional variants in other genes that may have also contributed to the phenotype (Thiadens et al., 2010; Langlo et al., 2016; Haer-Wigman et al., 2017); This variant is associated with the following publications: (PMID: 32913385, 30078014, 31456290, 27479814, 26355662, 20079539, 28224992)

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

Last Updated: Jul 15, 2024