NM_015443.4(KANSL1):c.2740G>A (p.Asp914Asn) AND Koolen-de Vries syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 22, 2023
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:: RCV003874395.1

Allele description

NM_015443.4(KANSL1):c.2740G>A (p.Asp914Asn)

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.2740G>A (p.Asp914Asn)

HGVS:

NC_000017.11:g.46033177C>T
NG_032784.1:g.197198G>A
NM_001193465.2:c.2737G>A
NM_001193466.2:c.2740G>A
NM_001379198.1:c.2740G>A
NM_001405854.1:c.2740G>A
NM_001405855.1:c.2740G>A
NM_001405856.1:c.2737G>A
NM_001405857.1:c.2737G>A
NM_001405858.1:c.2737G>A
NM_001405859.1:c.2638G>A
NM_001405860.1:c.2638G>A
NM_001405861.1:c.2635G>A
NM_001405872.1:c.2740G>A
NM_001405873.1:c.2740G>A
NM_001405874.1:c.2740G>A
NM_001405875.1:c.2551G>A
NM_001405876.1:c.2551G>A
NM_001405877.1:c.2551G>A
NM_001405878.1:c.2551G>A
NM_001405879.1:c.2548G>A
NM_001405880.1:c.2548G>A
NM_001405881.1:c.2635G>A
NM_001405882.1:c.1474G>A
NM_001405883.1:c.1471G>A
NM_001405884.1:c.1285G>A
NM_001405885.1:c.1282G>A
NM_015443.4:c.2740G>AMANE SELECT
NP_001180394.1:p.Asp913Asn
NP_001180395.1:p.Asp914Asn
NP_001366127.1:p.Asp914Asn
NP_001392783.1:p.Asp914Asn
NP_001392784.1:p.Asp914Asn
NP_001392785.1:p.Asp913Asn
NP_001392786.1:p.Asp913Asn
NP_001392787.1:p.Asp913Asn
NP_001392788.1:p.Asp880Asn
NP_001392789.1:p.Asp880Asn
NP_001392790.1:p.Asp879Asn
NP_001392801.1:p.Asp914Asn
NP_001392802.1:p.Asp914Asn
NP_001392803.1:p.Asp914Asn
NP_001392804.1:p.Asp851Asn
NP_001392805.1:p.Asp851Asn
NP_001392806.1:p.Asp851Asn
NP_001392807.1:p.Asp851Asn
NP_001392808.1:p.Asp850Asn
NP_001392809.1:p.Asp850Asn
NP_001392810.1:p.Asp879Asn
NP_001392811.1:p.Asp492Asn
NP_001392812.1:p.Asp491Asn
NP_001392813.1:p.Asp429Asn
NP_001392814.1:p.Asp428Asn
NP_056258.1:p.Asp914Asn
NC_000017.10:g.44110543C>T

Protein change:

D428N

Molecular consequence:

NM_001193465.2:c.2737G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001193466.2:c.2740G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379198.1:c.2740G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405854.1:c.2740G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405855.1:c.2740G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405856.1:c.2737G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405857.1:c.2737G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405858.1:c.2737G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405859.1:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405860.1:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405861.1:c.2635G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405872.1:c.2740G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405873.1:c.2740G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405874.1:c.2740G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405875.1:c.2551G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405876.1:c.2551G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405877.1:c.2551G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405878.1:c.2551G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405879.1:c.2548G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405880.1:c.2548G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405881.1:c.2635G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405882.1:c.1474G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405883.1:c.1471G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405884.1:c.1285G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001405885.1:c.1282G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015443.4:c.2740G>A - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004680313	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 22, 2023)	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

SCV004680313

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 22, 2023)

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 Invitae, SCV004680313.1

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

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 914 of the KANSL1 protein (p.Asp914Asn). This variant has not been reported in the literature in individuals affected with KANSL1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt KANSL1 protein function.

#	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: Mar 5, 2024

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