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NM_020366.4(RPGRIP1):c.1976A>G (p.Tyr659Cys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 16, 2017
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:
RCV000521905.1

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.1976A>G (p.Tyr659Cys)]

NM_020366.4(RPGRIP1):c.1976A>G (p.Tyr659Cys)

Gene:
RPGRIP1:RPGR interacting protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q11.2
Genomic location:
Preferred name:
NM_020366.4(RPGRIP1):c.1976A>G (p.Tyr659Cys)
HGVS:
  • NC_000014.9:g.21324831A>G
  • NG_008933.1:g.41855A>G
  • NM_001377523.1:c.689-2792A>G
  • NM_001377948.1:c.902A>G
  • NM_001377949.1:c.796+106A>G
  • NM_001377950.1:c.689-2792A>G
  • NM_001377951.1:c.191-2792A>G
  • NM_020366.4:c.1976A>GMANE SELECT
  • NP_001364877.1:p.Tyr301Cys
  • NP_065099.3:p.Tyr659Cys
  • NP_065099.3:p.Tyr659Cys
  • NC_000014.8:g.21792990A>G
  • NM_020366.3:c.1976A>G
Protein change:
Y301C
Links:
dbSNP: rs1278572461
NCBI 1000 Genomes Browser:
rs1278572461
Molecular consequence:
  • NM_001377523.1:c.689-2792A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377949.1:c.796+106A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377950.1:c.689-2792A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377951.1:c.191-2792A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377948.1:c.902A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020366.4:c.1976A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000618499GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jun 16, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000618499.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The Y659C variant in the RPGRIP1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The Y659C variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The Y659C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret Y659C as a variant of uncertain significance.

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

Last Updated: Sep 29, 2024