NM_022455.5(NSD1):c.3397A>G (p.Lys1133Glu) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 7, 2024
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:: RCV003994822.1

Allele description [Variation Report for NM_022455.5(NSD1):c.3397A>G (p.Lys1133Glu)]

NM_022455.5(NSD1):c.3397A>G (p.Lys1133Glu)

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.3397A>G (p.Lys1133Glu)

HGVS:

NC_000005.10:g.177211796A>G
NG_009821.1:g.83718A>G
NM_001365684.2:c.2524A>G
NM_001409301.1:c.3397A>G
NM_001409302.1:c.3397A>G
NM_001409303.1:c.3397A>G
NM_001409304.1:c.2977A>G
NM_001409305.1:c.2644A>G
NM_001409306.1:c.2524A>G
NM_001409307.1:c.2524A>G
NM_001409308.1:c.2524A>G
NM_001409309.1:c.2524A>G
NM_022455.4:c.3397A>G
NM_022455.5:c.3397A>GMANE SELECT
NM_172349.5:c.2524A>G
NP_001352613.1:p.Lys864Glu
NP_001352613.2:p.Lys842Glu
NP_001396230.1:p.Lys1133Glu
NP_001396231.1:p.Lys1133Glu
NP_001396232.1:p.Lys1133Glu
NP_001396233.1:p.Lys993Glu
NP_001396234.1:p.Lys882Glu
NP_001396235.1:p.Lys842Glu
NP_001396236.1:p.Lys842Glu
NP_001396237.1:p.Lys842Glu
NP_001396238.1:p.Lys842Glu
NP_071900.2:p.Lys1133Glu
NP_071900.2:p.Lys1133Glu
NP_758859.1:p.Lys864Glu
NP_758859.2:p.Lys842Glu
LRG_512t1:c.3397A>G
LRG_512:g.83718A>G
LRG_512p1:p.Lys1133Glu
NC_000005.9:g.176638797A>G
NM_001365684.1:c.2590A>G
NM_022455.4:c.3397A>G
NM_022455.5:c.3397A>G
NM_172349.3:c.2590A>G

Protein change:

K1133E

Links:

dbSNP: rs886060441

NCBI 1000 Genomes Browser:

rs886060441

Molecular consequence:

NM_001365684.2:c.2524A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409301.1:c.3397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409302.1:c.3397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409303.1:c.3397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409304.1:c.2977A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409305.1:c.2644A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409306.1:c.2524A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409307.1:c.2524A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409308.1:c.2524A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409309.1:c.2524A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_022455.5:c.3397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_172349.5:c.2524A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004813240	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Feb 7, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004813240

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Feb 7, 2024)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004813240.1

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

Description

Variant summary: NSD1 c.3397A>G (p.Lys1133Glu) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 251300 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.3397A>G in individuals affected with Sotos Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as 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: Apr 20, 2024

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