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NM_022455.5(NSD1):c.6655C>T (p.Arg2219Cys) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 7, 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:
RCV001583173.3

Allele description [Variation Report for NM_022455.5(NSD1):c.6655C>T (p.Arg2219Cys)]

NM_022455.5(NSD1):c.6655C>T (p.Arg2219Cys)

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.6655C>T (p.Arg2219Cys)
HGVS:
  • NC_000005.10:g.177294023C>T
  • NG_009821.1:g.165945C>T
  • NM_001365684.2:c.5782C>T
  • NM_001409301.1:c.6655C>T
  • NM_001409302.1:c.6655C>T
  • NM_001409303.1:c.6655C>T
  • NM_001409304.1:c.6235C>T
  • NM_001409305.1:c.5902C>T
  • NM_001409306.1:c.5893C>T
  • NM_001409307.1:c.5893C>T
  • NM_001409308.1:c.5782C>T
  • NM_001409309.1:c.5533C>T
  • NM_022455.5:c.6655C>TMANE SELECT
  • NM_172349.5:c.5782C>T
  • NP_001352613.1:p.Arg1950Cys
  • NP_001352613.2:p.Arg1928Cys
  • NP_001396230.1:p.Arg2219Cys
  • NP_001396231.1:p.Arg2219Cys
  • NP_001396232.1:p.Arg2219Cys
  • NP_001396233.1:p.Arg2079Cys
  • NP_001396234.1:p.Arg1968Cys
  • NP_001396235.1:p.Arg1965Cys
  • NP_001396236.1:p.Arg1965Cys
  • NP_001396237.1:p.Arg1928Cys
  • NP_001396238.1:p.Arg1845Cys
  • NP_071900.2:p.Arg2219Cys
  • NP_071900.2:p.Arg2219Cys
  • NP_758859.1:p.Arg1950Cys
  • NP_758859.2:p.Arg1928Cys
  • LRG_512t1:c.6655C>T
  • LRG_512:g.165945C>T
  • LRG_512p1:p.Arg2219Cys
  • NC_000005.9:g.176721024C>T
  • NM_001365684.1:c.5848C>T
  • NM_022455.4:c.6655C>T
  • NM_172349.3:c.5848C>T
Protein change:
R1845C
Links:
dbSNP: rs2127279650
NCBI 1000 Genomes Browser:
rs2127279650
Molecular consequence:
  • NM_001365684.2:c.5782C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409301.1:c.6655C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409302.1:c.6655C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409303.1:c.6655C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409304.1:c.6235C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409305.1:c.5902C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409306.1:c.5893C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409307.1:c.5893C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409308.1:c.5782C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409309.1:c.5533C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022455.5:c.6655C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172349.5:c.5782C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001810788GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Dec 7, 2020) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001810788.1

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

Description

Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; A different missense change at this residue (R2219H) has been reported at GeneDx in association with Sotos syndrome

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

Last Updated: Dec 24, 2023