NM_001193416.2(DDX3X):c.1462C>T (p.Arg488Cys) AND not provided

delete

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 28, 2015
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:: RCV000190111.1

Allele description

NM_001193416.2(DDX3X):c.1462C>T (p.Arg488Cys)

Gene:

DDX3X:DEAD-box helicase 3, X-linked [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001193416.2(DDX3X):c.1462C>T (p.Arg488Cys)

Other names:

p.R488C:CGC>TGC

HGVS:

NC_000023.11:g.41346375C>T
NG_012830.2:g.17978C>T
NM_001193416.2:c.1462C>T
NM_001193417.2:c.1414C>T
NM_001356.4:c.1462C>T
NP_001180345.1:p.Arg488Cys
NP_001180346.1:p.Arg472Cys
NP_001347.3:p.Arg488Cys
NC_000023.10:g.41205628C>T
NM_001193416.1:c.1462C>T
NM_001193417.1:c.1414C>T
NM_001356.3:c.1462C>T
NR_126093.1:n.2407C>T

Protein change:

R472C

Links:

dbSNP: rs796052234

NCBI 1000 Genomes Browser:

rs796052234

Molecular consequence:

NM_001356.4:c.1462C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_126093.1:n.2407C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:: MedGen: CN221809

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000240192	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 28, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000240192

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 28, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000240192.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

p.Arg488Cys (CGC>TGC): c.1462 C>T in exon 13 in the DDX3X Gene (NM_001356.3). The R488C variant in the DDX3X gene was not observed in approximately 6,500 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 R488C 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 within the Helicase C terminal that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret R488C as a pathogenic variant. This variant has been observed to be de novo with confirmed parentage.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 26, 2017

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