NM_001193466.2(KANSL1):c.19G>A (p.Ala7Thr) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Oct 9, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000187790.3

Allele description [Variation Report for NM_001193466.2(KANSL1):c.19G>A (p.Ala7Thr)]

NM_001193466.2(KANSL1):c.19G>A (p.Ala7Thr)

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.19G>A (p.Ala7Thr)
Other names:
p.A7T:GCT>ACT
HGVS:
  • NC_000017.11:g.46172125C>T
  • NG_032784.1:g.58250G>A
  • NM_001193465.1:c.19G>A
  • NM_001193466.2:c.19G>A
  • NM_015443.3:c.19G>A
  • NP_001180394.1:p.Ala7Thr
  • NP_001180395.1:p.Ala7Thr
  • NP_056258.1:p.Ala7Thr
  • NC_000017.10:g.44249491C>T
  • NM_001193466.1:c.19G>A
Protein change:
A7T
Links:
dbSNP: rs768152581
NCBI 1000 Genomes Browser:
rs768152581
Molecular consequence:
  • NM_001193465.1:c.19G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001193466.2:c.19G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015443.3:c.19G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000241387GeneDxcriteria provided, single submitter
Uncertain significance
(Mar 17, 2014)
germlineclinical testing

Citation Link,

SCV000831576Invitaecriteria provided, single submitter
Likely benign
(Oct 9, 2018)
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
not providedgermlineyesnot 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 GeneDx, SCV000241387.11

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

Description

This variant is denoted p.Ala7Thr (GCT>ACT): c.19 G>A in exon 2 of the KANSL1 gene (NM_001193466.1). The A7T variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The A7T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function; however missense mutations associated with KANSL1-related disorders have not been reported in this region of the protein. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in INFANT-EPI panel(s).

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

From Invitae, SCV000831576.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 14, 2021

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