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NM_017739.4(POMGNT1):c.1489C>G (p.Arg497Gly) AND Retinitis pigmentosa 76

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 24, 2023
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:
RCV002789966.2

Allele description [Variation Report for NM_017739.4(POMGNT1):c.1489C>G (p.Arg497Gly)]

NM_017739.4(POMGNT1):c.1489C>G (p.Arg497Gly)

Genes:
POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]
TSPAN1:tetraspanin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_017739.4(POMGNT1):c.1489C>G (p.Arg497Gly)
Other names:
NM_017739.4:c.1489C>G
HGVS:
  • NC_000001.11:g.46192148G>C
  • NG_009205.3:g.33158C>G
  • NM_001243766.2:c.1489C>G
  • NM_001290129.2:c.1423C>G
  • NM_001290130.2:c.1060C>G
  • NM_001410783.1:c.1489C>G
  • NM_017739.4:c.1489C>GMANE SELECT
  • NP_001230695.2:p.Arg497Gly
  • NP_001277058.2:p.Arg475Gly
  • NP_001277059.2:p.Arg354Gly
  • NP_001397712.1:p.Arg497Gly
  • NP_060209.4:p.Arg497Gly
  • LRG_701t1:c.1489C>G
  • LRG_701t2:c.1489C>G
  • LRG_701:g.33158C>G
  • LRG_701p1:p.Arg497Gly
  • LRG_701p2:p.Arg497Gly
  • NC_000001.10:g.46657820G>C
  • NR_024332.1:n.2140C>G
Protein change:
R354G
Molecular consequence:
  • NM_001243766.2:c.1489C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001290129.2:c.1423C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001290130.2:c.1060C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001410783.1:c.1489C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_017739.4:c.1489C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Retinitis pigmentosa 76 (RP76)
Identifiers:
MONDO: MONDO:0014929; MedGen: C4310704; OMIM: 617123

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003761207Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 24, 2023) 		germlinecuration

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761207.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The heterozygous p.Arg497Gly variant in POMGNT1 was identified by our study in one individual with retinal dystrophy. This individual also carried another variant of uncertain significance in POMGNT1; however, the phase of these variants is unknown at this time. The p.Arg497Gly variant in POMGNT1 has not been previously reported in the literature in individuals with POMGNT1-associated retinal dystrophy. This variant was absent from large population studies. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Arg497Gly variant is uncertain. ACMG/AMP Criteria applied: PM2_Supporting, PP3 (Richards 2015).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 30, 2024