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NM_015443.4(KANSL1):c.1412_1413del (p.Lys471fs) AND Koolen-de Vries syndrome

Clinical significance:Likely pathogenic (Last evaluated: Jan 3, 2022)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001807912.1

Allele description [Variation Report for NM_015443.4(KANSL1):c.1412_1413del (p.Lys471fs)]

NM_015443.4(KANSL1):c.1412_1413del (p.Lys471fs)

Gene:
KANSL1:KAT8 regulatory NSL complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17q21.31
Genomic location:
Preferred name:
NM_015443.4(KANSL1):c.1412_1413del (p.Lys471fs)
HGVS:
  • NC_000017.11:g.46094579_46094580del
  • NG_032784.1:g.135796_135797del
  • NM_001193465.2:c.1412_1413del
  • NM_001193466.2:c.1412_1413del
  • NM_001379198.1:c.1412_1413del
  • NM_015443.4:c.1412_1413delMANE SELECT
  • NP_001180394.1:p.Lys471fs
  • NP_001180395.1:p.Lys471fs
  • NP_001366127.1:p.Lys471fs
  • NP_056258.1:p.Lys471fs
  • NC_000017.10:g.44171945_44171946del
Protein change:
K471fs
Molecular consequence:
  • NM_001193465.2:c.1412_1413del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001193466.2:c.1412_1413del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001379198.1:c.1412_1413del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_015443.4:c.1412_1413del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Koolen-de Vries syndrome (KDVS)
Synonyms:
KANSL1-Related Intellectual Disability Syndrome
Identifiers:
MONDO: MONDO:0012496; MedGen: C1864871; Orphanet: 96169; OMIM: 610443

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV0020581863billioncriteria provided, single submitter
Likely pathogenic
(Jan 3, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

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 3billion, SCV002058186.1

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

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Jun 3, 2022

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