NM_022455.5(NSD1):c.805G>A (p.Glu269Lys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 30, 2017
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:: RCV000520028.8

Allele description [Variation Report for NM_022455.5(NSD1):c.805G>A (p.Glu269Lys)]

NM_022455.5(NSD1):c.805G>A (p.Glu269Lys)

Gene:

NSD1:nuclear receptor binding SET domain protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_022455.5(NSD1):c.805G>A (p.Glu269Lys)

HGVS:

NC_000005.10:g.177135908G>A
NG_009821.1:g.7830G>A
NM_001365684.2:c.-36-33G>A
NM_001409301.1:c.805G>A
NM_001409302.1:c.805G>A
NM_001409303.1:c.805G>A
NM_001409304.1:c.418-33G>A
NM_001409305.1:c.-36-33G>A
NM_001409306.1:c.-36-33G>A
NM_001409307.1:c.-36-33G>A
NM_001409308.1:c.-36-33G>A
NM_001409309.1:c.-36-33G>A
NM_022455.5:c.805G>AMANE SELECT
NM_172349.5:c.-36-33G>A
NP_001396230.1:p.Glu269Lys
NP_001396231.1:p.Glu269Lys
NP_001396232.1:p.Glu269Lys
NP_071900.2:p.Glu269Lys
NP_071900.2:p.Glu269Lys
LRG_512t1:c.805G>A
LRG_512:g.7830G>A
LRG_512p1:p.Glu269Lys
NC_000005.9:g.176562909G>A
NM_022455.4:c.805G>A

Protein change:

E269K

Links:

dbSNP: rs751787444

NCBI 1000 Genomes Browser:

rs751787444

Molecular consequence:

NM_001365684.2:c.-36-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001409304.1:c.418-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001409305.1:c.-36-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001409306.1:c.-36-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001409307.1:c.-36-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001409308.1:c.-36-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001409309.1:c.-36-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_172349.5:c.-36-33G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001409301.1:c.805G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409302.1:c.805G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409303.1:c.805G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_022455.5:c.805G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000621721	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Oct 30, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000621721

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Oct 30, 2017)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000621721.1

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

Description

The E269K variant in the NSD1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The E269K variant is observed in 1/111,614 (0.001%) alleles from individuals of non-Finnish European background in large population cohorts (Lek et al., 2016). The E269K variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret E269K as a variant of uncertain significance.

#	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: Nov 10, 2024

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