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NM_001356.5(DDX3X):c.1535_1536del (p.His512fs) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
May 9, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000190107.17

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)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000240188GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Oct 28, 2021)
germlineclinical testing

Citation Link,

SCV001580879Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(May 9, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From GeneDx, SCV000240188.13

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31618753, 26235985, 28135719, 30817323, 32371413)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001580879.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 207812). This premature translational stop signal has been observed in individual(s) with X-linked intellectual disability (PMID: 26235985). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.His512Argfs*5) in the DDX3X gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DDX3X are known to be pathogenic (PMID: 26235985).

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

Last Updated: Oct 26, 2024