NM_015443.4(KANSL1):c.808_816del (p.Leu270_Ser272del) AND Koolen-de Vries syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 14, 2021
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:: RCV001904856.5

Allele description [Variation Report for NM_015443.4(KANSL1):c.808_816del (p.Leu270_Ser272del)]

NM_015443.4(KANSL1):c.808_816del (p.Leu270_Ser272del)

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.808_816del (p.Leu270_Ser272del)

HGVS:

NC_000017.11:g.46171330_46171338del
NG_032784.1:g.59039_59047del
NM_001193465.2:c.808_816del
NM_001193466.2:c.808_816del
NM_001379198.1:c.808_816del
NM_015443.4:c.808_816delMANE SELECT
NP_001180394.1:p.Leu270_Ser272del
NP_001180395.1:p.Leu270_Ser272del
NP_001366127.1:p.Leu270_Ser272del
NP_056258.1:p.Leu270_Ser272del
NC_000017.10:g.44248694_44248702del
NC_000017.10:g.44248696_44248704del

Links:

dbSNP: rs2046275378

NCBI 1000 Genomes Browser:

rs2046275378

Molecular consequence:

NM_001193465.2:c.808_816del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001193466.2:c.808_816del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001379198.1:c.808_816del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_015443.4:c.808_816del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV002126841	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 14, 2021)	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

SCV002126841

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 14, 2021)

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, SCV002126841.2

#	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. This variant, c.808_816del, results in the deletion of 3 amino acid(s) of the KANSL1 protein (p.Leu270_Ser272del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases (ExAC) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. This variant has not been reported in the literature in individuals with KANSL1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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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