NM_001298.3(CNGA3):c.829C>T (p.Arg277Cys) AND Achromatopsia 2

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: May 4, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000010089.10

Allele description [Variation Report for NM_001298.3(CNGA3):c.829C>T (p.Arg277Cys)]

NM_001298.3(CNGA3):c.829C>T (p.Arg277Cys)

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.829C>T (p.Arg277Cys)

HGVS:

NC_000002.12:g.98395999C>T
NG_009097.1:g.54845C>T
NM_001079878.2:c.775C>T
NM_001298.3:c.829C>TMANE SELECT
NP_001073347.1:p.Arg259Cys
NP_001289.1:p.Arg277Cys
NP_001289.1:p.Arg277Cys
NC_000002.11:g.99012462C>T
NM_001298.2:c.829C>T
Q16281:p.Arg277Cys

Protein change:

R259C; ARG277CYS

Links:

UniProtKB: Q16281#VAR_047579; OMIM: 600053.0009; dbSNP: rs104893620

NCBI 1000 Genomes Browser:

rs104893620

Molecular consequence:

NM_001079878.2:c.775C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001298.3:c.829C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Achromatopsia 2 (ACHM2)
Synonyms:: Colorblindness, total; Rod monochromatism 2; Rod monochromacy 2
Identifiers:: MONDO: MONDO:0009003; MedGen: C1857618; Orphanet: 49382; OMIM: 216900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000030310	OMIM	no assertion criteria provided	Pathogenic (Oct 1, 2001)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV001524042	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 9, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002518728	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link,
SCV002782956	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 25, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

CNGA3 mutations in hereditary cone photoreceptor disorders.

Wissinger B, Gamer D, Jägle H, Giorda R, Marx T, Mayer S, Tippmann S, Broghammer M, Jurklies B, Rosenberg T, Jacobson SG, Sener EC, Tatlipinar S, Hoyng CB, Castellan C, Bitoun P, Andreasson S, Rudolph G, Kellner U, Lorenz B, Wolff G, Verellen-Dumoulin C, et al.

Am J Hum Genet. 2001 Oct;69(4):722-37. Epub 2001 Aug 30.

PubMed [citation]

PMID:: 11536077
PMCID:: PMC1226059

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From OMIM, SCV000030310.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In patients with rod monochromacy (ACHM2; 216900), Wissinger et al. (2001) identified a C-to-T transition at nucleotide 829 of the CNGA3 gene, resulting in an arg277-to-cys (R277C) substitution; the mutation was found in 9 of 110 mutant alleles.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001524042.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mendelics, SCV002518728.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002782956.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 12, 2024

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