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NM_015443.4(KANSL1):c.2470C>T (p.Arg824Ter) AND KANSL1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 15, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003403743.5

Allele description [Variation Report for NM_015443.4(KANSL1):c.2470C>T (p.Arg824Ter)]

NM_015443.4(KANSL1):c.2470C>T (p.Arg824Ter)

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_015443.4(KANSL1):c.2470C>T (p.Arg824Ter)
Other names:
NM_015443.4(KANSL1):c.2470C>T; p.Arg824Ter
HGVS:
  • NC_000017.11:g.46038609G>A
  • NG_032784.1:g.191766C>T
  • NM_001193465.2:c.2470C>T
  • NM_001193466.2:c.2470C>T
  • NM_001379198.1:c.2470C>T
  • NM_015443.4:c.2470C>TMANE SELECT
  • NP_001180394.1:p.Arg824Ter
  • NP_001180395.1:p.Arg824Ter
  • NP_001366127.1:p.Arg824Ter
  • NP_056258.1:p.Arg824Ter
  • NC_000017.10:g.44115975G>A
  • NC_000017.10:g.44115975G>A
  • NM_001193466.1:c.2470C>T
Protein change:
R824*
Links:
dbSNP: rs2077221203
NCBI 1000 Genomes Browser:
rs2077221203
Molecular consequence:
  • NM_001193465.2:c.2470C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001193466.2:c.2470C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001379198.1:c.2470C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015443.4:c.2470C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
KANSL1-related disorder
Synonyms:
KANSL1-related condition
Identifiers:

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004112101PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jul 15, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004112101.2

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

Description

The KANSL1 c.2470C>T variant is predicted to result in premature protein termination (p.Arg824*). This variant has been documented as de novo in a patient with Koolen De Vries syndrome (Case 5 in Prat et al. 2021. PubMed ID: 33393407). This variant has not been reported in gnomAD, indicating this variant is rare. This variant falls within a highly paralogous region. Allele frequency data should be interpreted with caution. Nonsense variants in KANSL1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Oct 13, 2024