NM_015443.4(KANSL1):c.3116C>T (p.Thr1039Ile) AND Koolen-de Vries syndrome

Clinical significance:Uncertain significance (Last evaluated: Dec 13, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000554702.2

Allele description [Variation Report for NM_015443.4(KANSL1):c.3116C>T (p.Thr1039Ile)]

NM_015443.4(KANSL1):c.3116C>T (p.Thr1039Ile)

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.3116C>T (p.Thr1039Ile)
HGVS:
  • NC_000017.11:g.46031678G>A
  • NG_032784.1:g.198697C>T
  • NM_001193465.2:c.3113C>T
  • NM_001193466.2:c.3116C>T
  • NM_001379198.1:c.3116C>T
  • NM_015443.4:c.3116C>TMANE SELECT
  • NP_001180394.1:p.Thr1038Ile
  • NP_001180395.1:p.Thr1039Ile
  • NP_001366127.1:p.Thr1039Ile
  • NP_056258.1:p.Thr1039Ile
  • NC_000017.10:g.44109044G>A
  • NM_001193466.1:c.3116C>T
Protein change:
T1038I
Links:
dbSNP: rs1444239074
NCBI 1000 Genomes Browser:
rs1444239074
Molecular consequence:
  • NM_001193465.2:c.3113C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001193466.2:c.3116C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379198.1:c.3116C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015443.4:c.3116C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Koolen-de Vries syndrome (KDVS)
Synonyms:
17q21.31 microdeletion syndrome; 17q21.31 deletion syndrome; Monosomy 17q21.31; See all synonyms [MedGen]
Identifiers:
MedGen: C1864871; Orphanet: 96169; OMIM: 610443

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000645059Invitaecriteria provided, single submitter
Uncertain significance
(Dec 13, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000645059.3

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

Description

This sequence change replaces threonine with isoleucine at codon 1039 of the KANSL1 protein (p.Thr1039Ile). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a KANSL1-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Possibly Damaging; Align-GVGD: Class C0). In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance.

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

Last Updated: Nov 27, 2021

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