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NM_001356.5(DDX3X):c.1535_1536del (p.His512fs) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 27, 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:
RCV002317665.9

Allele description [Variation Report for NM_001356.5(DDX3X):c.1535_1536del (p.His512fs)]

NM_001356.5(DDX3X):c.1535_1536del (p.His512fs)

Gene:
DDX3X:DEAD-box helicase 3 X-linked [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001356.5(DDX3X):c.1535_1536del (p.His512fs)
HGVS:
  • NC_000023.11:g.41346542_41346543del
  • NG_012830.2:g.18145_18146del
  • NM_001193416.3:c.1535_1536del
  • NM_001193417.3:c.1487_1488del
  • NM_001356.5:c.1535_1536delMANE SELECT
  • NM_001363819.1:c.977_978del
  • NP_001180345.1:p.His512fs
  • NP_001180346.1:p.His496fs
  • NP_001347.3:p.His512fs
  • NP_001350748.1:p.His326fs
  • NC_000023.10:g.41205795_41205796del
  • NC_000023.10:g.41205795_41205796delAT
  • NM_001193416.1:c.1535_1536del
  • NM_001193416.1:c.1535_1536delAT
  • NM_001356.3:c.1535_1536delAT
  • NM_001356.4:c.1535_1536del
  • NM_001356.4:c.1535_1536delAT
  • NR_126093.1:n.2480_2481del
  • p.H512Rfs*5
Protein change:
H326fs
Links:
OMIM: 300160.0013; dbSNP: rs796052230
NCBI 1000 Genomes Browser:
rs796052230
Molecular consequence:
  • NM_001193416.3:c.1535_1536del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001193417.3:c.1487_1488del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001356.5:c.1535_1536del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001363819.1:c.977_978del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_126093.1:n.2480_2481del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000849460Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Jul 27, 2018) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling.

Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders MR, Venselaar H, Helsmoortel C, Cho MT, Hoischen A, Vissers LE, Koemans TS, Wissink-Lindhout W, Eichler EE, Romano C, Van Esch H, Stumpel C, Vreeburg M, Smeets E, Oberndorff K, van Bon BW, Shaw M, et al.

Am J Hum Genet. 2015 Aug 6;97(2):343-52. doi: 10.1016/j.ajhg.2015.07.004. Epub 2015 Jul 30.

PubMed [citation]
PMID:
26235985
PMCID:
PMC4573244

Details of each submission

From Ambry Genetics, SCV000849460.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.1535_1536delAT pathogenic mutation, located in coding exon 14 of the DDX3X gene, results from a deletion of two nucleotides at nucleotide positions 1535 to 1536, causing a translational frameshift with a predicted alternate stop codon (p.H512Rfs*5). This alteration was detected as a de novo occurrence in two females with mild-to-moderate intellectual disability, hypotonia, ventricular enlargement, and precocious puberty (Snijders Blok L et al. Am. J. Hum. Genet., 2015 Aug;97:343-52). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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

Last Updated: Sep 29, 2024