NM_015443.4(KANSL1):c.3164A>G (p.Asp1055Gly) AND Koolen-de Vries syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 13, 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:: RCV003052056.3

Allele description [Variation Report for NM_015443.4(KANSL1):c.3164A>G (p.Asp1055Gly)]

NM_015443.4(KANSL1):c.3164A>G (p.Asp1055Gly)

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.3164A>G (p.Asp1055Gly)

HGVS:

NC_000017.11:g.46031630T>C
NG_032784.1:g.198745A>G
NM_001193465.2:c.3161A>G
NM_001193466.2:c.3164A>G
NM_001379198.1:c.3164A>G
NM_001405854.1:c.3164A>G
NM_001405855.1:c.3164A>G
NM_001405856.1:c.3161A>G
NM_001405857.1:c.3161A>G
NM_001405858.1:c.3161A>G
NM_001405859.1:c.3062A>G
NM_001405860.1:c.3062A>G
NM_001405861.1:c.3059A>G
NM_001405872.1:c.3032A>G
NM_001405873.1:c.3032A>G
NM_001405874.1:c.3032A>G
NM_001405875.1:c.2975A>G
NM_001405876.1:c.2975A>G
NM_001405877.1:c.2975A>G
NM_001405878.1:c.2975A>G
NM_001405879.1:c.2972A>G
NM_001405880.1:c.2972A>G
NM_001405881.1:c.2927A>G
NM_001405882.1:c.1898A>G
NM_001405883.1:c.1895A>G
NM_001405884.1:c.1709A>G
NM_001405885.1:c.1706A>G
NM_015443.4:c.3164A>GMANE SELECT
NP_001180394.1:p.Asp1054Gly
NP_001180395.1:p.Asp1055Gly
NP_001366127.1:p.Asp1055Gly
NP_001392783.1:p.Asp1055Gly
NP_001392784.1:p.Asp1055Gly
NP_001392785.1:p.Asp1054Gly
NP_001392786.1:p.Asp1054Gly
NP_001392787.1:p.Asp1054Gly
NP_001392788.1:p.Asp1021Gly
NP_001392789.1:p.Asp1021Gly
NP_001392790.1:p.Asp1020Gly
NP_001392801.1:p.Asp1011Gly
NP_001392802.1:p.Asp1011Gly
NP_001392803.1:p.Asp1011Gly
NP_001392804.1:p.Asp992Gly
NP_001392805.1:p.Asp992Gly
NP_001392806.1:p.Asp992Gly
NP_001392807.1:p.Asp992Gly
NP_001392808.1:p.Asp991Gly
NP_001392809.1:p.Asp991Gly
NP_001392810.1:p.Asp976Gly
NP_001392811.1:p.Asp633Gly
NP_001392812.1:p.Asp632Gly
NP_001392813.1:p.Asp570Gly
NP_001392814.1:p.Asp569Gly
NP_056258.1:p.Asp1055Gly
NC_000017.10:g.44108996T>C

Protein change:

D1011G

Molecular consequence:

NM_001193465.2:c.3161A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001193466.2:c.3164A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379198.1:c.3164A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405854.1:c.3164A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405855.1:c.3164A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405856.1:c.3161A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405857.1:c.3161A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405858.1:c.3161A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405859.1:c.3062A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405860.1:c.3062A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405861.1:c.3059A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405872.1:c.3032A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405873.1:c.3032A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405874.1:c.3032A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405875.1:c.2975A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405876.1:c.2975A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405877.1:c.2975A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405878.1:c.2975A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405879.1:c.2972A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405880.1:c.2972A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405881.1:c.2927A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405882.1:c.1898A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405883.1:c.1895A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405884.1:c.1709A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405885.1:c.1706A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015443.4:c.3164A>G - 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
SCV003352436	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 13, 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

SCV003352436

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 13, 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, SCV003352436.2

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 1055 of the KANSL1 protein (p.Asp1055Gly). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KANSL1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.

#	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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