NM_015443.4(KANSL1):c.658A>T (p.Thr220Ser) AND Koolen-de Vries syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001243816.8

Allele description [Variation Report for NM_015443.4(KANSL1):c.658A>T (p.Thr220Ser)]

NM_015443.4(KANSL1):c.658A>T (p.Thr220Ser)

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.658A>T (p.Thr220Ser)

HGVS:

NC_000017.11:g.46171486T>A
NG_032784.1:g.58889A>T
NM_001193465.2:c.658A>T
NM_001193466.2:c.658A>T
NM_001379198.1:c.658A>T
NM_015443.4:c.658A>TMANE SELECT
NP_001180394.1:p.Thr220Ser
NP_001180395.1:p.Thr220Ser
NP_001366127.1:p.Thr220Ser
NP_056258.1:p.Thr220Ser
NC_000017.10:g.44248852T>A
NM_001193466.1:c.658A>T

Protein change:

T220S

Links:

dbSNP: rs2046287355

NCBI 1000 Genomes Browser:

rs2046287355

Molecular consequence:

NM_001193465.2:c.658A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001193466.2:c.658A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379198.1:c.658A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015443.4:c.658A>T - missense variant - [Sequence Ontology: SO:0001583]

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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Chain B, PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
Chain B, PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
gi|119389036|pdb|2C0M|B

Protein
Chain C, PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
Chain C, PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
gi|119389037|pdb|2C0M|C

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001416999	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001416999

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001416999.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Due to the possible presence of a polymorphic segmental duplication, the location of the variant could not be unambiguously resolved. Variants with ambiguous mapping are still reported relative to the KANSL1 transcript. Until the location of this sequence change can be resolved, the clinical significance of this variant remains uncertain. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 968633). This variant has not been reported in the literature in individuals with KANSL1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 220 of the KANSL1 protein (p.Thr220Ser).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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