NM_001379270.1(CNGA1):c.640C>T (p.Arg214Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 4, 2024
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:: RCV001054103.7

Allele description [Variation Report for NM_001379270.1(CNGA1):c.640C>T (p.Arg214Ter)]

NM_001379270.1(CNGA1):c.640C>T (p.Arg214Ter)

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.640C>T (p.Arg214Ter)

HGVS:

NC_000004.12:g.47940775G>A
NG_009193.1:g.77170C>T
NM_000087.5:c.640C>T
NM_001142564.2:c.640C>T
NM_001379270.1:c.640C>TMANE SELECT
NP_000078.3:p.Arg214Ter
NP_001136036.1:p.Arg287Ter
NP_001136036.2:p.Arg214Ter
NP_001366199.1:p.Arg214Ter
NC_000004.11:g.47942792G>A
NM_000087.3:c.652C>T
NM_000087.4:c.652C>T
NM_001142564.1:c.859C>T

Protein change:

R214*

Links:

dbSNP: rs759781200

NCBI 1000 Genomes Browser:

rs759781200

Molecular consequence:

NM_000087.5:c.640C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142564.2:c.640C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001379270.1:c.640C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001218399	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 4, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25326637, 29785639, 26496393, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001218399

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 4, 2024)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Clinical exome sequencing for genetic identification of rare Mendelian disorders.

Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CG, Dipple KM, Grody WW, Vilain E, Nelson SF.

JAMA. 2014 Nov 12;312(18):1880-7. doi: 10.1001/jama.2014.14604.

PubMed [citation]

PMID:: 25326637
PMCID:: PMC4278636

Development of a molecular diagnostic test for Retinitis Pigmentosa in the Japanese population.

Maeda A, Yoshida A, Kawai K, Arai Y, Akiba R, Inaba A, Takagi S, Fujiki R, Hirami Y, Kurimoto Y, Ohara O, Takahashi M.

Jpn J Ophthalmol. 2018 Jul;62(4):451-457. doi: 10.1007/s10384-018-0601-x. Epub 2018 May 21.

PubMed [citation]

PMID:: 29785639

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001218399.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Arg218*) in the CNGA1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 473 amino acid(s) of the CNGA1 protein. This variant is present in population databases (rs759781200, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with retinitis pigmentosa (PMID: 25326637, 29785639). ClinVar contains an entry for this variant (Variation ID: 242520). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts a region of the CNGA1 protein in which other variant(s) (p.Arg424*, p.Arg493*) have been determined to be pathogenic (PMID: 26496393). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	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: Jun 9, 2024

ClinVar

Relating variation to medicine