NM_015443.4(KANSL1):c.487A>G (p.Lys163Glu) AND Koolen-de Vries syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Oct 19, 2020
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:: RCV002470414.1

Allele description [Variation Report for NM_015443.4(KANSL1):c.487A>G (p.Lys163Glu)]

NM_015443.4(KANSL1):c.487A>G (p.Lys163Glu)

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.487A>G (p.Lys163Glu)

HGVS:

NC_000017.11:g.46171657T>C
NG_032784.1:g.58718A>G
NM_001193465.2:c.487A>G
NM_001193466.2:c.487A>G
NM_001379198.1:c.487A>G
NM_001405854.1:c.487A>G
NM_001405855.1:c.487A>G
NM_001405856.1:c.487A>G
NM_001405857.1:c.487A>G
NM_001405858.1:c.487A>G
NM_001405859.1:c.487A>G
NM_001405860.1:c.487A>G
NM_001405861.1:c.487A>G
NM_001405872.1:c.487A>G
NM_001405873.1:c.487A>G
NM_001405874.1:c.487A>G
NM_001405875.1:c.487A>G
NM_001405876.1:c.487A>G
NM_001405877.1:c.487A>G
NM_001405878.1:c.487A>G
NM_001405879.1:c.487A>G
NM_001405880.1:c.487A>G
NM_001405881.1:c.487A>G
NM_015443.4:c.487A>GMANE SELECT
NP_001180394.1:p.Lys163Glu
NP_001180395.1:p.Lys163Glu
NP_001366127.1:p.Lys163Glu
NP_001392783.1:p.Lys163Glu
NP_001392784.1:p.Lys163Glu
NP_001392785.1:p.Lys163Glu
NP_001392786.1:p.Lys163Glu
NP_001392787.1:p.Lys163Glu
NP_001392788.1:p.Lys163Glu
NP_001392789.1:p.Lys163Glu
NP_001392790.1:p.Lys163Glu
NP_001392801.1:p.Lys163Glu
NP_001392802.1:p.Lys163Glu
NP_001392803.1:p.Lys163Glu
NP_001392804.1:p.Lys163Glu
NP_001392805.1:p.Lys163Glu
NP_001392806.1:p.Lys163Glu
NP_001392807.1:p.Lys163Glu
NP_001392808.1:p.Lys163Glu
NP_001392809.1:p.Lys163Glu
NP_001392810.1:p.Lys163Glu
NP_056258.1:p.Lys163Glu
NC_000017.10:g.44249023T>C
NM_001193466.1:c.487A>G

Protein change:

K163E

Molecular consequence:

NM_001193465.2:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001193466.2:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379198.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405854.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405855.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405856.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405857.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405858.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405859.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405860.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405861.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405872.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405873.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405874.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405875.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405876.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405877.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405878.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405879.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405880.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001405881.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015443.4:c.487A>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

Recent activity

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SRP434425 (0)
SRA
outer membrane secretory protein [Salmonella enterica subsp. enterica serovar Ty...
outer membrane secretory protein [Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344]
gi|301157929|emb|CBW17424.1|

Protein
ribonuclease D [Serratia marcescens]
ribonuclease D [Serratia marcescens]
gi|1216666646|gnl|PRJNA357595|BVG96 0|gb|ASL97993.1|

Protein
conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typh...
conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344]
gi|301156636|emb|CBW16106.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002767821	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Oct 19, 2020)	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

SCV002767821

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Oct 19, 2020)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767821.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Likely Benign. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Koolen-De Vries syndrome (MIM#610443). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from lysine to glutamic acid. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0503 - Missense variant consistently predicted to be tolerated by multiple in silico tools or not conserved in placental mammals with a minor amino acid change. (SB) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants in the same codon have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1206 - This variant has been shown to be paternally inherited (VCGS #18G003318 by segregation analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Dec 24, 2022

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