chrX-41334294-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP6_Moderate
The NM_001356.5(DDX3X):c.42G>C(p.Gln14His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 24)
Consequence
DDX3X
NM_001356.5 missense
NM_001356.5 missense
Scores
7
5
Clinical Significance
Conservation
PhyloP100: 8.37
Genes affected
DDX3X (HGNC:2745): (DEAD-box helicase 3 X-linked) The protein encoded by this gene is a member of the large DEAD-box protein family, that is defined by the presence of the conserved Asp-Glu-Ala-Asp (DEAD) motif, and has ATP-dependent RNA helicase activity. This protein has been reported to display a high level of RNA-independent ATPase activity, and unlike most DEAD-box helicases, the ATPase activity is thought to be stimulated by both RNA and DNA. This protein has multiple conserved domains and is thought to play roles in both the nucleus and cytoplasm. Nuclear roles include transcriptional regulation, mRNP assembly, pre-mRNA splicing, and mRNA export. In the cytoplasm, this protein is thought to be involved in translation, cellular signaling, and viral replication. Misregulation of this gene has been implicated in tumorigenesis. This gene has a paralog located in the nonrecombining region of the Y chromosome. Pseudogenes sharing similarity to both this gene and the DDX3Y paralog are found on chromosome 4 and the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, DDX3X
BP6
?
Variant X-41334294-G-C is Benign according to our data. Variant chrX-41334294-G-C is described in ClinVar as [Benign]. Clinvar id is 1693000.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX3X | NM_001356.5 | c.42G>C | p.Gln14His | missense_variant | 1/17 | ENST00000644876.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX3X | ENST00000644876.2 | c.42G>C | p.Gln14His | missense_variant | 1/17 | NM_001356.5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome ? Cov.: 24
GnomAD4 genome
?
Cov.:
24
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, X-linked 102 Benign:1
Benign, criteria provided, single submitter | clinical testing | Pars Genome Lab | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Uncertain
D;D;.;T;.;.;.;.;.;.;.;.;.
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.;M;.;.;.;.;.;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
Polyphen
P;P;.;.;.;.;.;.;.;.;.;.;.
Vest4
0.47, 0.46, 0.46, 0.55, 0.90, 0.47
MutPred
Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);Gain of catalytic residue at Q14 (P = 0.1199);
MVP
0.78
MPC
1.6
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.