X-41334294-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP2 BP6_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
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

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

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 24

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Intellectual disability, X-linked 102 Benign:1

Benign, criteria provided, single submitter

clinical testing

Pars Genome Lab

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Benign	-0.087	T
BayesDel_noAF	Benign	-0.36
Cadd	Uncertain	25
Dann	Uncertain	0.99
DEOGEN2	Uncertain	0.50	D;D;.;T;.;.;.;.;.;.;.;.;.
FATHMM_MKL	Uncertain	0.92	D
M_CAP	Benign	0.060	D
MetaRNN	Uncertain	0.50	T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Uncertain	2.7	M;M;.;.;M;.;.;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.75	T
Polyphen		0.53	P;P;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.47, 0.46, 0.46, 0.55, 0.90, 0.47
MutPred		0.57		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		0.96	D
GERP RS		4.3
Varity_R		0.55
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-41193547;