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NM_022552.5(DNMT3A):c.2657del (p.Gln886fs) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 29, 2018
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:
RCV001008921.1

Allele description [Variation Report for NM_022552.5(DNMT3A):c.2657del (p.Gln886fs)]

NM_022552.5(DNMT3A):c.2657del (p.Gln886fs)

Gene:
DNMT3A:DNA methyltransferase 3 alpha [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p23.3
Genomic location:
Preferred name:
NM_022552.5(DNMT3A):c.2657del (p.Gln886fs)
HGVS:
  • NC_000002.12:g.25234361del
  • NG_029465.2:g.113230del
  • NM_001320893.1:c.2201del
  • NM_001375819.1:c.1988del
  • NM_022552.5:c.2657delMANE SELECT
  • NM_153759.3:c.2090del
  • NM_175629.2:c.2657del
  • NP_001307822.1:p.Gln734fs
  • NP_001362748.1:p.Gln663fs
  • NP_072046.2:p.Gln886fs
  • NP_715640.2:p.Gln697fs
  • NP_783328.1:p.Gln886fs
  • LRG_459t2:c.2090del
  • LRG_459t4:c.2657del
  • LRG_459:g.113230del
  • LRG_459p2:p.Gln697fs
  • LRG_459p4:p.Gln886fs
  • NC_000002.11:g.25457230del
  • NM_175629.2:c.2657delA
  • NR_135490.2:n.3087del
Protein change:
Q663fs
Links:
dbSNP: rs1573291900
NCBI 1000 Genomes Browser:
rs1573291900
Molecular consequence:
  • NM_001320893.1:c.2201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001375819.1:c.1988del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_022552.5:c.2657del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_153759.3:c.2090del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_175629.2:c.2657del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_135490.2:n.3087del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001168727GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jun 29, 2018) 		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, SCV001168727.1

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

Description

A variant that is likely pathogenic has been identified in the DNMT3A gene. The c.2657delA variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.2657delA variant causes a frameshift starting with codon Glutamine 886, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 20 of the new reading frame, denoted p.Gln886ArgfsX20. This frameshift variant is predicted to result in protein truncation as the last 27 amino acids are lost and replaced with 19 incorrect amino acids. The c.2657delA variant is not observed in large population cohorts (Lek et al., 2016). Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

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

Last Updated: Apr 23, 2022