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NM_015443.4(KANSL1):c.1042C>T (p.Arg348Ter) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 5, 2024
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:
RCV000622541.4

Allele description [Variation Report for NM_015443.4(KANSL1):c.1042C>T (p.Arg348Ter)]

NM_015443.4(KANSL1):c.1042C>T (p.Arg348Ter)

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.1042C>T (p.Arg348Ter)
HGVS:
  • NC_000017.11:g.46171102G>A
  • NG_032784.1:g.59273C>T
  • NM_001193465.2:c.1042C>T
  • NM_001193466.2:c.1042C>T
  • NM_001379198.1:c.1042C>T
  • NM_015443.4:c.1042C>TMANE SELECT
  • NP_001180394.1:p.Arg348Ter
  • NP_001180394.1:p.Arg348Ter
  • NP_001180395.1:p.Arg348Ter
  • NP_001366127.1:p.Arg348Ter
  • NP_056258.1:p.Arg348Ter
  • NC_000017.10:g.44248468G>A
  • NM_001193465.1:c.1042C>T
  • NM_001193466.1:c.1042C>T
  • NM_001193466.2:c.1042C>T
Protein change:
R348*
Links:
dbSNP: rs1427624649
NCBI 1000 Genomes Browser:
rs1427624649
Molecular consequence:
  • NM_001193465.2:c.1042C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001193466.2:c.1042C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001379198.1:c.1042C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015443.4:c.1042C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000742382Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Apr 5, 2024) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Intragenic KANSL1 mutations and chromosome 17q21.31 deletions: broadening the clinical spectrum and genotype-phenotype correlations in a large cohort of patients.

Zollino M, Marangi G, Ponzi E, Orteschi D, Ricciardi S, Lattante S, Murdolo M, Battaglia D, Contaldo I, Mercuri E, Stefanini MC, Caumes R, Edery P, Rossi M, Piccione M, Corsello G, Della Monica M, Scarano F, Priolo M, Gentile M, Zampino G, Vijzelaar R, et al.

J Med Genet. 2015 Dec;52(12):804-14. doi: 10.1136/jmedgenet-2015-103184. Epub 2015 Sep 30.

PubMed [citation]
PMID:
26424144

Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience.

Miller CR, Lee K, Pfau RB, Reshmi SC, Corsmeier DJ, Hashimoto S, Dave-Wala A, Jayaraman V, Koboldt D, Matthews T, Mouhlas D, Stein M, McKinney A, Grossman T, Kelly BJ, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE.

Cold Spring Harb Mol Case Stud. 2020 Jun 12;6(3). doi:pii: a005231. 10.1101/mcs.a005231. Print 2020 Jun.

PubMed [citation]
PMID:
32371413
PMCID:
PMC7304353
See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000742382.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

The c.1042C>T (p.R348*) alteration, located in exon 2 (coding exon 1) of the KANSL1 gene, consists of a C to T substitution at nucleotide position 1042. This changes the amino acid from an arginine (R) to a stop codon at amino acid position 348. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been detected in multiple individuals with Koolen-de Vries syndrome, including multiple cases of reported de novo occurrence (Zollino, 2015; Miller, 2020; St John, 2022). Based on the available evidence, this alteration is classified as pathogenic.

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

Last Updated: Aug 11, 2024