NM_001193466.2(KANSL1):c.1826G>A (p.Ser609Asn) AND Koolen-de Vries syndrome

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Dec 5, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000474219.7

Allele description [Variation Report for NM_001193466.2(KANSL1):c.1826G>A (p.Ser609Asn)]

NM_001193466.2(KANSL1):c.1826G>A (p.Ser609Asn)

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.1826G>A (p.Ser609Asn)
HGVS:
  • NC_000017.11:g.46066559C>T
  • NG_032784.1:g.163816G>A
  • NM_001193465.1:c.1826G>A
  • NM_001193466.2:c.1826G>A
  • NM_015443.3:c.1826G>A
  • NP_001180394.1:p.Ser609Asn
  • NP_001180395.1:p.Ser609Asn
  • NP_056258.1:p.Ser609Asn
  • NC_000017.10:g.44143925C>T
  • NM_001193466.1:c.1826G>A
Protein change:
S609N
Links:
dbSNP: rs138698439
NCBI 1000 Genomes Browser:
rs138698439
Molecular consequence:
  • NM_001193465.1:c.1826G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001193466.2:c.1826G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015443.3:c.1826G>A - 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
SCV000559733Invitaecriteria provided, single submitter
Benign
(Dec 5, 2020)
germlineclinical testing

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

SCV000898763Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicagocriteria provided, single submitter
Uncertain significance
(Oct 11, 2017)
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Invitae, SCV000559733.6

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

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV000898763.1

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

Description

KANSL1 NM_001193466.1 exon 6 p.Ser609Asn (c.1826G>A): This variant has not been reported in the literature but is present in 0.4% (115/24030) of African alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs138698439). This variant is present in ClinVar (Variation ID:376914). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Sep 18, 2021

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