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NM_022455.5(NSD1):c.3089T>C (p.Leu1030Ser) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
May 2, 2022
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:
RCV002512581.9

Allele description [Variation Report for NM_022455.5(NSD1):c.3089T>C (p.Leu1030Ser)]

NM_022455.5(NSD1):c.3089T>C (p.Leu1030Ser)

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.3089T>C (p.Leu1030Ser)
HGVS:
  • NC_000005.10:g.177211488T>C
  • NG_009821.1:g.83410T>C
  • NM_001365684.2:c.2216T>C
  • NM_001409301.1:c.3089T>C
  • NM_001409302.1:c.3089T>C
  • NM_001409303.1:c.3089T>C
  • NM_001409304.1:c.2669T>C
  • NM_001409305.1:c.2336T>C
  • NM_001409306.1:c.2216T>C
  • NM_001409307.1:c.2216T>C
  • NM_001409308.1:c.2216T>C
  • NM_001409309.1:c.2216T>C
  • NM_022455.5:c.3089T>CMANE SELECT
  • NM_172349.5:c.2216T>C
  • NP_001352613.1:p.Leu761Ser
  • NP_001352613.2:p.Leu739Ser
  • NP_001396230.1:p.Leu1030Ser
  • NP_001396231.1:p.Leu1030Ser
  • NP_001396232.1:p.Leu1030Ser
  • NP_001396233.1:p.Leu890Ser
  • NP_001396234.1:p.Leu779Ser
  • NP_001396235.1:p.Leu739Ser
  • NP_001396236.1:p.Leu739Ser
  • NP_001396237.1:p.Leu739Ser
  • NP_001396238.1:p.Leu739Ser
  • NP_071900.2:p.Leu1030Ser
  • NP_071900.2:p.Leu1030Ser
  • NP_758859.1:p.Leu761Ser
  • NP_758859.2:p.Leu739Ser
  • LRG_512t1:c.3089T>C
  • LRG_512:g.83410T>C
  • LRG_512p1:p.Leu1030Ser
  • NC_000005.9:g.176638489T>C
  • NM_001365684.1:c.2282T>C
  • NM_022455.4:c.3089T>C
  • NM_172349.3:c.2282T>C
Protein change:
L1030S
Links:
dbSNP: rs200856103
NCBI 1000 Genomes Browser:
rs200856103
Molecular consequence:
  • NM_001365684.2:c.2216T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409301.1:c.3089T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409302.1:c.3089T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409303.1:c.3089T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409304.1:c.2669T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409305.1:c.2336T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409306.1:c.2216T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409307.1:c.2216T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409308.1:c.2216T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001409309.1:c.2216T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022455.5:c.3089T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172349.5:c.2216T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003658680Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(May 2, 2022) 		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 Ambry Genetics, SCV003658680.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Nov 10, 2024