NM_001379270.1(CNGA1):c.1743_1746del (p.Thr582fs) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 29, 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:: RCV001236237.5

Allele description

NM_001379270.1(CNGA1):c.1743_1746del (p.Thr582fs)

Genes:

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

Variant type:

Deletion

Cytogenetic location:

4p12

Genomic location:

Preferred name:

NM_001379270.1(CNGA1):c.1743_1746del (p.Thr582fs)

HGVS:

NC_000004.12:g.47936738_47936741del
NG_009193.1:g.81206_81209del
NM_000087.5:c.1743_1746del
NM_001142564.2:c.1743_1746del
NM_001379270.1:c.1743_1746delMANE SELECT
NP_000078.3:p.Thr582fs
NP_001136036.2:p.Thr582fs
NP_001366199.1:p.Thr582fs
NC_000004.11:g.47938753_47938756del
NC_000004.11:g.47938755_47938758del
NM_000087.3:c.1755_1758del
NM_000087.3:c.1755_1758delAACT
NM_001142564.1:c.1962_1965del

Protein change:

T582fs

Links:

dbSNP: rs768694789

NCBI 1000 Genomes Browser:

rs768694789

Molecular consequence:

NM_000087.5:c.1743_1746del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142564.2:c.1743_1746del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001379270.1:c.1743_1746del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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small nuclear ribonucleoprotein E isoform 2 [Homo sapiens]
small nuclear ribonucleoprotein E isoform 2 [Homo sapiens]
gi|751130453|ref|NP_001291393.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001408952	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 29, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 28981474, 7479749, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001408952

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 29, 2024)

germline

clinical testing

PubMed (3)
[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

The Genetic Basis of Pericentral Retinitis Pigmentosa-A Form of Mild Retinitis Pigmentosa.

Comander J, Weigel-DiFranco C, Maher M, Place E, Wan A, Harper S, Sandberg MA, Navarro-Gomez D, Pierce EA.

Genes (Basel). 2017 Oct 5;8(10). doi:pii: E256. 10.3390/genes8100256.

PubMed [citation]

PMID:: 28981474
PMCID:: PMC5664106

Mutations in the gene encoding the alpha subunit of the rod cGMP-gated channel in autosomal recessive retinitis pigmentosa.

Dryja TP, Finn JT, Peng YW, McGee TL, Berson EL, Yau KW.

Proc Natl Acad Sci U S A. 1995 Oct 24;92(22):10177-81.

PubMed [citation]

PMID:: 7479749
PMCID:: PMC40759

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001408952.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Thr586Serfs*17) in the CNGA1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 105 amino acid(s) of the CNGA1 protein. This variant is present in population databases (rs768694789, gnomAD 0.004%). This premature translational stop signal has been observed in individual(s) with retinitis pigmentosa (PMID: 28981474). ClinVar contains an entry for this variant (Variation ID: 866019). This variant disrupts a region of the CNGA1 protein in which other variant(s) (p.Arg658Aspfs*2) have been determined to be pathogenic (PMID: 7479749; Invitae). 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 23, 2024

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