NM_015443.4(KANSL1):c.868C>T (p.Arg290Ter) AND Koolen-de Vries syndrome

Clinical significance:Pathogenic (Last evaluated: Mar 19, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000678306.1

Allele description [Variation Report for NM_015443.4(KANSL1):c.868C>T (p.Arg290Ter)]

NM_015443.4(KANSL1):c.868C>T (p.Arg290Ter)

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.868C>T (p.Arg290Ter)
HGVS:
  • NC_000017.11:g.46171276G>A
  • NG_032784.1:g.59099C>T
  • NM_001193465.2:c.868C>T
  • NM_001193466.2:c.868C>T
  • NM_001379198.1:c.868C>T
  • NM_015443.4:c.868C>TMANE SELECT
  • NP_001180394.1:p.Arg290Ter
  • NP_001180395.1:p.Arg290Ter
  • NP_001366127.1:p.Arg290Ter
  • NP_056258.1:p.Arg290Ter
  • NC_000017.10:g.44248642G>A
  • NM_001193466.1:c.868C>T
Protein change:
R290*
Links:
dbSNP: rs149830411
NCBI 1000 Genomes Browser:
rs149830411
Molecular consequence:
  • NM_001193465.2:c.868C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001193466.2:c.868C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001379198.1:c.868C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015443.4:c.868C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

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
SCV000804365Geisinger Autism and Developmental Medicine Institute,Geisinger Health Systemcriteria provided, single submitter
Pathogenic
(Mar 19, 2018)
unknownprovider interpretation, clinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot provided1not providedclinical testing, provider interpretation

Citations

PubMed

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 Geisinger Autism and Developmental Medicine Institute,Geisinger Health System, SCV000804365.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedprovider interpretation PubMed (1)
2not provided1not providednot providedclinical testing PubMed (1)

Description

This variant was identified in a 12 year old female with a history of intellectual disability, hypotonia, short stature, atrial septal defect, patent ductus arteriosus, multicystic dysplastic left kidney, congenital valgus foot deformity, constipation, and dysphagia. Dysmorphic facial features include coarse facies, hypertelorism, epicanthal folds, broad nasal tip, and wide spaced teeth. The variant is present in the gnomAD Finnish population at 0.058% but is absent from all other populations with sufficient data. The presence of an inversion polymorphism at 17q21.31 which overlaps KANSL1 complicates the interpretation of this variant. The proband is adopted and parental samples were not available. However, there was very strong clinical correlation between this patient's clinical features and Koolen-DeVries syndrome. In addition, whole exome sequencing identified an additional VUS in a gene of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided
2unknownyes1not providednot provided1not providednot providednot provided

Last Updated: Oct 25, 2021

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