NM_001193416.2(DDX3X):c.1667T>C (p.Leu556Ser) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Dec 24, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description

NM_001193416.2(DDX3X):c.1667T>C (p.Leu556Ser)

DDX3X:DEAD-box helicase 3 X-linked [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001193416.2(DDX3X):c.1667T>C (p.Leu556Ser)
  • NC_000023.11:g.41346910T>C
  • NG_012830.2:g.18513T>C
  • NM_001193416.2:c.1667T>C
  • NM_001356.4:c.1667T>C
  • NP_001180345.1:p.Leu556Ser
  • NP_001347.3:p.Leu556Ser
  • NC_000023.10:g.41206163T>C
  • NM_001193416.1:c.1667T>C
Protein change:
dbSNP: rs1057521175
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001356.4:c.1667T>C - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000521464GeneDxcriteria provided, single submitter
Likely pathogenic
(Dec 24, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000521464.3

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


The L556S variant in the DDX3X gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The L556S variant was not observed in approximately 6,400 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The L556S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. The L556S variant is a strong candidate for a pathogenic variant.

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

Last Updated: Sep 14, 2018