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NM_152281.3(GORAB):c.118C>T (p.Arg40Ter) AND Geroderma osteodysplastica

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 30, 2018
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:
RCV000778948.4

Allele description [Variation Report for NM_152281.3(GORAB):c.118C>T (p.Arg40Ter)]

NM_152281.3(GORAB):c.118C>T (p.Arg40Ter)

Gene:
GORAB:golgin, RAB6 interacting [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q24.2
Genomic location:
Preferred name:
NM_152281.3(GORAB):c.118C>T (p.Arg40Ter)
HGVS:
  • NC_000001.11:g.170539266C>T
  • NG_012237.1:g.12145C>T
  • NM_001146039.2:c.118C>T
  • NM_001320252.2:c.-348C>T
  • NM_152281.3:c.118C>TMANE SELECT
  • NP_001139511.2:p.Arg40Ter
  • NP_689494.2:p.Arg65Ter
  • NP_689494.3:p.Arg40Ter
  • NC_000001.10:g.170508407C>T
  • NM_152281.2:c.193C>T
  • NR_027397.2:n.176C>T
Protein change:
R40*
Links:
dbSNP: rs369967804
NCBI 1000 Genomes Browser:
rs369967804
Molecular consequence:
  • NM_001320252.2:c.-348C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_027397.2:n.176C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001146039.2:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152281.3:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Geroderma osteodysplastica (GO)
Synonyms:
Walt Disney dwarfism
Identifiers:
MONDO: MONDO:0009271; MedGen: C0432255; Orphanet: 2078; OMIM: 231070

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000915370Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)		Uncertain significance
(Nov 30, 2018) 		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 Illumina Laboratory Services, Illumina, SCV000915370.1

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

Description

The GORAB c.193C>T (p.Arg65Ter) variant is a stop-gained variant, predicted to result in premature termination of the protein. The variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018) and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score for this variant, it could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. Due to the potential impact of stop-gained variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for geroderma osteodysplasticum.

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

Last Updated: Mar 5, 2024