NM_001379270.1(CNGA1):c.2018T>C (p.Ile673Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 26, 2022
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:: RCV003092020.1

Allele description [Variation Report for NM_001379270.1(CNGA1):c.2018T>C (p.Ile673Thr)]

NM_001379270.1(CNGA1):c.2018T>C (p.Ile673Thr)

Genes:

CNGA1:cyclic nucleotide gated channel subunit alpha 1 [Gene - OMIM - HGNC]
LOC101927157:uncharacterized LOC101927157 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

4p12

Genomic location:

Preferred name:

NM_001379270.1(CNGA1):c.2018T>C (p.Ile673Thr)

HGVS:

NC_000004.12:g.47936464A>G
NG_009193.1:g.81481T>C
NM_000087.3:c.2030T>C
NM_000087.5:c.2018T>C
NM_001142564.2:c.2018T>C
NM_001375386.1:c.2030T>C
NM_001379270.1:c.2018T>CMANE SELECT
NP_000078.3:p.Ile673Thr
NP_001136036.2:p.Ile673Thr
NP_001362315.1:p.Ile677Thr
NP_001366199.1:p.Ile673Thr
NC_000004.11:g.47938481A>G

Protein change:

I673T

Molecular consequence:

NM_000087.5:c.2018T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142564.2:c.2018T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375386.1:c.2030T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001379270.1:c.2018T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PIG-M [Eurytemora carolleeae]
PIG-M [Eurytemora carolleeae]
Gene ID:111710146

Gene
LOC105563684 [Vollenhovia emeryi]
LOC105563684 [Vollenhovia emeryi]
Gene ID:105563684

Gene
Rtp3 receptor transporter protein 3 [Mus musculus]
Rtp3 receptor transporter protein 3 [Mus musculus]
Gene ID:235636

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003482243	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 26, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003482243

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 26, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Invitae, SCV003482243.1

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

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 677 of the CNGA1 protein (p.Ile677Thr). This variant is present in population databases (rs562189832, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with CNGA1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

Last Updated: May 1, 2024

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