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NM_015272.5(RPGRIP1L):c.2239C>T (p.Arg747Ter) AND Joubert syndrome and related disorders

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 25, 2022
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:
RCV002469441.1

Allele description [Variation Report for NM_015272.5(RPGRIP1L):c.2239C>T (p.Arg747Ter)]

NM_015272.5(RPGRIP1L):c.2239C>T (p.Arg747Ter)

Gene:
RPGRIP1L:RPGRIP1 like [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q12.2
Genomic location:
Preferred name:
NM_015272.5(RPGRIP1L):c.2239C>T (p.Arg747Ter)
HGVS:
  • NC_000016.10:g.53649029G>A
  • NG_008991.2:g.59831C>T
  • NM_001127897.4:c.2239C>T
  • NM_001308334.3:c.2239C>T
  • NM_001330538.2:c.2239C>T
  • NM_015272.5:c.2239C>TMANE SELECT
  • NP_001121369.1:p.Arg747Ter
  • NP_001295263.1:p.Arg747Ter
  • NP_001317467.1:p.Arg747Ter
  • NP_056087.2:p.Arg747Ter
  • LRG_696t1:c.2239C>T
  • LRG_696t2:c.2239C>T
  • LRG_696:g.59831C>T
  • LRG_696p1:p.Arg747Ter
  • LRG_696p2:p.Arg747Ter
  • NC_000016.9:g.53682941G>A
  • NM_015272.4:c.2239C>T
  • NM_015272.5:c.2239C>T
Protein change:
R747*
Links:
dbSNP: rs767686118
NCBI 1000 Genomes Browser:
rs767686118
Molecular consequence:
  • NM_001127897.4:c.2239C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001308334.3:c.2239C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001330538.2:c.2239C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015272.5:c.2239C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Joubert syndrome and related disorders
Identifiers:
MONDO: MONDO:0015369; MedGen: C5679612

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002766382Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Nov 25, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002766382.1

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

Description

Variant summary: RPGRIP1L c.2239C>T (p.Arg747X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 4e-06 in 251386 control chromosomes (gnomAD). To our knowledge, no occurrence of c.2239C>T in individuals affected with Joubert Syndrome And Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Sep 29, 2024