NM_001193466.2(KANSL1):c.868C>T (p.Arg290Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Dec 13, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000486096.1

Allele description [Variation Report for NM_001193466.2(KANSL1):c.868C>T (p.Arg290Ter)]

NM_001193466.2(KANSL1):c.868C>T (p.Arg290Ter)

Gene:
KANSL1:KAT8 regulatory NSL complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.31
Genomic location:
Preferred name:
NM_001193466.2(KANSL1):c.868C>T (p.Arg290Ter)
HGVS:
  • NC_000017.11:g.46171276G>A
  • NG_032784.1:g.59099C>T
  • NM_001193465.1:c.868C>T
  • NM_001193466.2:c.868C>T
  • NM_015443.3:c.868C>T
  • NP_001180394.1:p.Arg290Ter
  • NP_001180395.1:p.Arg290Ter
  • NP_056258.1:p.Arg290Ter
  • NC_000017.10:g.44248642G>A
  • NM_001193466.1:c.868C>T
Protein change:
R290*
Links:
dbSNP: rs149830411
NCBI 1000 Genomes Browser:
rs149830411
Molecular consequence:
  • NM_001193465.1:c.868C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001193466.2:c.868C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015443.3:c.868C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000570441GeneDxcriteria provided, single submitter
Pathogenic
(Dec 13, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000570441.3

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

Description

The R290X variant in the KANSL1 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 R290X variant is observed in 16/277,204 alleles in large population cohorts, however, the reported allele frequency is likely from the inverted haplotype (Lek et al., 2016). We interpret R290X as a pathogenic variant.

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

Last Updated: Apr 12, 2021

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