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NM_022455.5(NSD1):c.6009+1G>T AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 2, 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:
RCV000522702.1

Allele description [Variation Report for NM_022455.5(NSD1):c.6009+1G>T]

NM_022455.5(NSD1):c.6009+1G>T

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.6009+1G>T
HGVS:
  • NC_000005.10:g.177282582G>T
  • NG_009821.1:g.154504G>T
  • NM_001365684.2:c.5136+1G>T
  • NM_001409301.1:c.6009+1G>T
  • NM_001409302.1:c.6009+1G>T
  • NM_001409303.1:c.6009+1G>T
  • NM_001409304.1:c.5589+1G>T
  • NM_001409305.1:c.5256+1G>T
  • NM_001409306.1:c.5247+1G>T
  • NM_001409307.1:c.5247+1G>T
  • NM_001409308.1:c.5136+1G>T
  • NM_001409309.1:c.5136+1G>T
  • NM_022455.5:c.6009+1G>TMANE SELECT
  • NM_172349.5:c.5136+1G>T
  • LRG_512t1:c.6009+1G>T
  • LRG_512:g.154504G>T
  • NC_000005.9:g.176709583G>T
  • NM_022455.4:c.6009+1G>T
Links:
dbSNP: rs1554204648
NCBI 1000 Genomes Browser:
rs1554204648
Molecular consequence:
  • NM_001365684.2:c.5136+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409301.1:c.6009+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409302.1:c.6009+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409303.1:c.6009+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409304.1:c.5589+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409305.1:c.5256+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409306.1:c.5247+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409307.1:c.5247+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409308.1:c.5136+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001409309.1:c.5136+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_022455.5:c.6009+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_172349.5:c.5136+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000621356GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Oct 2, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000621356.2

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

Description

The c.6009+1 G>T splice site variant in the NSD1 gene destroys the canonical splice donor site in intron 19. It has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is not observed in large population cohorts (Lek et al., 2016). It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. However, in the absence of RNA/functional studies, the actual effect of this sequence change is unknown. In summary, we consider this variant to be likely pathogenic.

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

Last Updated: Jun 10, 2023