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NM_001356.5(DDX3X):c.544-8_544-6del AND Intellectual disability, X-linked 102

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 16, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001310275.3

Allele description [Variation Report for NM_001356.5(DDX3X):c.544-8_544-6del]

NM_001356.5(DDX3X):c.544-8_544-6del

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.544-8_544-6del
HGVS:
  • NC_000023.11:g.41343208_41343210del
  • NG_012830.2:g.14811_14813del
  • NM_001193416.3:c.544-8_544-6del
  • NM_001193417.3:c.496-8_496-6del
  • NM_001356.5:c.544-8_544-6delMANE SELECT
  • NM_001363819.1:c.-15-8_-15-6del
  • NC_000023.10:g.41202461_41202463del
  • NM_001193416.3:c.544-10_544-8delTTC
Links:
dbSNP: rs2063875026
NCBI 1000 Genomes Browser:
rs2063875026
Molecular consequence:
  • NM_001193416.3:c.544-8_544-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001193417.3:c.496-8_496-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001356.5:c.544-8_544-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363819.1:c.-15-8_-15-6del - intron variant - [Sequence Ontology: SO:0001627]
Functional consequence:
sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071]
Observations:
1

Condition(s)

Name:
Intellectual disability, X-linked 102 (MRXSSB)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, SNIJDERS BLOK TYPE
Identifiers:
MONDO: MONDO:0010497; MedGen: C5393299; Orphanet: 457260; OMIM: 300958

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001499890HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP)
no assertion criteria provided
Likely pathogenic
(Oct 16, 2020) 		de novoclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Caucasiande novoyes1not providednot providednot providednot providedclinical testing

Details of each submission

From HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP), SCV001499890.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedclinical testingnot provided

Description

The c.544-10_544-8del variant in the DDX3X gene (NM_001193416.3) is a deletion of three nucleotides of intron 6. The in-silico tools predict that it is very likely to affect conventional splicing. This alteration has not been reported previously in the literature, however, in HGMD (ID: CD208594) an equivalent deletion is registered as pathological (c.544-8_544-6delCTT). Pathological variants in the DDX3X gene are associated with the phenotype of "Disorder of intellectual development X-linked Snijders Blok type "(OMIM: 300958). Therefore, the clinical significance of the c.544-10_544-8del variant is likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 23, 2024