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NM_022455.5(NSD1):c.3220C>T (p.Arg1074Cys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 11, 2023
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:
RCV003235633.8

Allele description [Variation Report for NM_022455.5(NSD1):c.3220C>T (p.Arg1074Cys)]

NM_022455.5(NSD1):c.3220C>T (p.Arg1074Cys)

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.3220C>T (p.Arg1074Cys)
HGVS:
  • NC_000005.10:g.177211619C>T
  • NG_009821.1:g.83541C>T
  • NM_001365684.2:c.2347C>T
  • NM_001409301.1:c.3220C>T
  • NM_001409302.1:c.3220C>T
  • NM_001409303.1:c.3220C>T
  • NM_001409304.1:c.2800C>T
  • NM_001409305.1:c.2467C>T
  • NM_001409306.1:c.2347C>T
  • NM_001409307.1:c.2347C>T
  • NM_001409308.1:c.2347C>T
  • NM_001409309.1:c.2347C>T
  • NM_022455.5:c.3220C>TMANE SELECT
  • NM_172349.5:c.2347C>T
  • NP_001352613.1:p.Arg805Cys
  • NP_001352613.2:p.Arg783Cys
  • NP_001396230.1:p.Arg1074Cys
  • NP_001396231.1:p.Arg1074Cys
  • NP_001396232.1:p.Arg1074Cys
  • NP_001396233.1:p.Arg934Cys
  • NP_001396234.1:p.Arg823Cys
  • NP_001396235.1:p.Arg783Cys
  • NP_001396236.1:p.Arg783Cys
  • NP_001396237.1:p.Arg783Cys
  • NP_001396238.1:p.Arg783Cys
  • NP_071900.2:p.Arg1074Cys
  • NP_071900.2:p.Arg1074Cys
  • NP_758859.1:p.Arg805Cys
  • NP_758859.2:p.Arg783Cys
  • LRG_512t1:c.3220C>T
  • LRG_512:g.83541C>T
  • LRG_512p1:p.Arg1074Cys
  • NC_000005.9:g.176638620C>T
  • NM_001365684.1:c.2413C>T
  • NM_022455.4:c.3220C>T
  • NM_172349.3:c.2413C>T
Protein change:
R1074C
Links:
dbSNP: rs775044010
NCBI 1000 Genomes Browser:
rs775044010
Molecular consequence:
  • NM_001365684.2:c.2347C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409301.1:c.3220C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409302.1:c.3220C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409303.1:c.3220C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409304.1:c.2800C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409305.1:c.2467C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409306.1:c.2347C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409307.1:c.2347C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409308.1:c.2347C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409309.1:c.2347C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022455.5:c.3220C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172349.5:c.2347C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003934009Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(May 11, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003934009.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: NSD1 c.3220C>T (p.Arg1074Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 3.6e-05 in 250766 control chromosomes (gnomAD). 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.3220C>T in individuals affected with Sotos Syndrome 1 and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter has assessed the variant since 2014: the variant was classified as benign. Based on the evidence outlined above, the variant was classified as uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024