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NM_015559.3(SETBP1):c.666G>A (p.Trp222Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 27, 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:
RCV000760674.1

Allele description [Variation Report for NM_015559.3(SETBP1):c.666G>A (p.Trp222Ter)]

NM_015559.3(SETBP1):c.666G>A (p.Trp222Ter)

Gene:
SETBP1:SET binding protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q12.3
Genomic location:
Preferred name:
NM_015559.3(SETBP1):c.666G>A (p.Trp222Ter)
HGVS:
  • NC_000018.10:g.44950006G>A
  • NG_027527.2:g.274834G>A
  • NM_015559.3:c.666G>AMANE SELECT
  • NP_056374.2:p.Trp222Ter
  • LRG_1150t1:c.666G>A
  • LRG_1150:g.274834G>A
  • LRG_1150p1:p.Trp222Ter
  • NC_000018.9:g.42529971G>A
  • NM_015559.2:c.666G>A
Protein change:
W222*
Links:
dbSNP: rs1391600900
NCBI 1000 Genomes Browser:
rs1391600900
Molecular consequence:
  • NM_015559.3:c.666G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000890566GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Jul 27, 2018) 		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, SCV000890566.1

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

Description

The W222X variant in the SETBP1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The W222X variant is not observed in large population cohorts (Lek et al., 2016). We interpret W222X as a pathogenic variant,

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

Last Updated: Aug 5, 2023