NM_001379270.1(CNGA1):c.1312T>G (p.Trp438Gly) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 16, 2021
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:: RCV000998236.29

Allele description [Variation Report for NM_001379270.1(CNGA1):c.1312T>G (p.Trp438Gly)]

NM_001379270.1(CNGA1):c.1312T>G (p.Trp438Gly)

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.1312T>G (p.Trp438Gly)

HGVS:

NC_000004.12:g.47937170A>C
NG_009193.1:g.80775T>G
NM_000087.5:c.1312T>G
NM_001142564.2:c.1312T>G
NM_001379270.1:c.1312T>GMANE SELECT
NP_000078.3:p.Trp438Gly
NP_001136036.2:p.Trp438Gly
NP_001366199.1:p.Trp438Gly
NC_000004.11:g.47939187A>C
NM_000087.3:c.1324T>G

Protein change:

W438G

Links:

dbSNP: rs200583020

NCBI 1000 Genomes Browser:

rs200583020

Molecular consequence:

NM_000087.5:c.1312T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142564.2:c.1312T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379270.1:c.1312T>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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uncharacterized protein At4g38062-like [Cucurbita pepo subsp. pepo]
uncharacterized protein At4g38062-like [Cucurbita pepo subsp. pepo]
gi|1333173017|ref|XP_023517616.1|

Protein
MLO-like protein 12 [Cucurbita moschata]
MLO-like protein 12 [Cucurbita moschata]
gi|1279831648|ref|XP_022926097.1|

Protein
ADP-ribosylation factor GTPase-activating protein AGD12-like [Cucurbita moschata...
ADP-ribosylation factor GTPase-activating protein AGD12-like [Cucurbita moschata]
gi|1279832870|ref|XP_022926731.1|

Protein
pentatricopeptide repeat-containing protein At4g35850, mitochondrial [Cucumis sa...
pentatricopeptide repeat-containing protein At4g35850, mitochondrial [Cucumis sativus]
gi|449446722|ref|XP_004141120.1|

Protein
unnamed protein product [Prunus armeniaca]
unnamed protein product [Prunus armeniaca]
gi|1866908335|emb|CAB4312335.1||gnl CAEK|CAB4312335

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001154190	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Feb 1, 2018)	germline	clinical testing	Citation Link,
SCV001206183	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 16, 2021)	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

SCV001154190

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Feb 1, 2018)

germline

clinical testing

Citation Link,

SCV001206183

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 16, 2021)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing
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 CeGaT Center for Human Genetics Tuebingen, SCV001154190.27

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001206183.5

#	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 tryptophan, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 442 of the CNGA1 protein (p.Trp442Gly). This variant is present in population databases (rs200583020, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with CNGA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 809634). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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: Oct 20, 2024

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