NM_001356.5(DDX3X):c.1675CTT[1] (p.Leu560del) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jul 15, 2022
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:: RCV000599287.31

Allele description [Variation Report for NM_001356.5(DDX3X):c.1675CTT[1] (p.Leu560del)]

NM_001356.5(DDX3X):c.1675CTT[1] (p.Leu560del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001356.5(DDX3X):c.1675CTT[1] (p.Leu560del)

HGVS:

NC_000023.11:g.41346918CTT[1]
NG_012830.2:g.18521CTT[1]
NM_001193416.3:c.1675CTT[1]
NM_001193417.3:c.1627CTT[1]
NM_001356.5:c.1675CTT[1]MANE SELECT
NM_001363819.1:c.1117CTT[1]
NP_001180345.1:p.Leu560del
NP_001180346.1:p.Leu544del
NP_001347.3:p.Leu560del
NP_001350748.1:p.Leu374del
NC_000023.10:g.41206171CTT[1]
NM_001193416.1:c.1678_1680del
NM_001193416.1:c.1678_1680delCTT
NM_001356.4:c.1678_1680del
NM_001356.5:c.1678_1680delMANE SELECT
NR_126093.1:n.2620CTT[1]
p.Leu560del

Protein change:

L374del

Links:

dbSNP: rs1555954380

NCBI 1000 Genomes Browser:

rs1555954380

Molecular consequence:

NM_001193416.3:c.1675CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001193417.3:c.1627CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001356.5:c.1675CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001363819.1:c.1117CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_126093.1:n.2620CTT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000710020	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jul 15, 2022)	germline	clinical testing	Citation Link,
SCV001250517	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jul 1, 2021)	germline	clinical testing	Citation Link,
SCV002064508	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 12, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000710020

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jul 15, 2022)

germline

clinical testing

Citation Link,

SCV001250517

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jul 1, 2021)

germline

clinical testing

Citation Link,

SCV002064508

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 12, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000710020.5

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

Description

Not observed in large population cohorts (gnomAD); In-frame deletion of one amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 26235985, 31278258)

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001250517.27

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

#	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		2	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV002064508.1

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

#	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: Jan 26, 2025

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