NM_000541.5(SAG):c.874C>T (p.Arg292Ter) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 15, 2023
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:: RCV001389455.10

Allele description [Variation Report for NM_000541.5(SAG):c.874C>T (p.Arg292Ter)]

NM_000541.5(SAG):c.874C>T (p.Arg292Ter)

Gene:

SAG:S-antigen visual arrestin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q37.1

Genomic location:

Preferred name:

NM_000541.5(SAG):c.874C>T (p.Arg292Ter)

HGVS:

NC_000002.12:g.233335029C>T
NG_009116.1:g.32367C>T
NM_000541.5:c.874C>TMANE SELECT
NP_000532.2:p.Arg292Ter
NC_000002.11:g.234243675C>T
NM_000541.4:c.874C>T
NM_000541.4:c.[874C>T]

Protein change:

R292*; ARG292TER

Links:

OMIM: 181031.0004; dbSNP: rs397514681

NCBI 1000 Genomes Browser:

rs397514681

Molecular consequence:

NM_000541.5:c.874C>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
SCV001590833	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 15, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 22581970, 9452120, 15234147, 22665972, 28492532
SCV002019984	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 14, 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

SCV001590833

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 15, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV002019984

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 14, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A paradigm shift in the delivery of services for diagnosis of inherited retinal disease.

O'Sullivan J, Mullaney BG, Bhaskar SS, Dickerson JE, Hall G, O'Grady A, Webster A, Ramsden SC, Black GC.

J Med Genet. 2012 May;49(5):322-6. doi: 10.1136/jmedgenet-2012-100847.

PubMed [citation]

PMID:: 22581970

Two Indian siblings with Oguchi disease are homozygous for an arrestin mutation encoding premature termination.

Maw M, Kumaramanickavel G, Kar B, John S, Bridges R, Denton M.

Hum Mutat. 1998;Suppl 1:S317-9. No abstract available.

PubMed [citation]

PMID:: 9452120

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001590833.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 41897). This premature translational stop signal has been observed in individuals with autosomal recessive retinitis pigmentosa and Oguchi disease (PMID: 15234147, 22581970). This variant is present in population databases (rs397514681, gnomAD 0.04%). This sequence change creates a premature translational stop signal (p.Arg292*) in the SAG gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SAG are known to be pathogenic (PMID: 9452120, 15234147, 22665972).

#	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 Revvity Omics, Revvity, SCV002019984.3

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 19, 2024

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