NC_000005.9:g.(?_176935330)_(176942071_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 22, 2022
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:: RCV003119723.3

Allele description [Variation Report for NC_000005.9:g.(?_176935330)_(176942071_?)del]

NC_000005.9:g.(?_176935330)_(176942071_?)del

Genes:: DDX41:DEAD-box helicase 41 [Gene - OMIM - HGNC]
DOK3:docking protein 3 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 5q35.3
Genomic location:: Chr5: 176935330 - 176942071 (on Assembly GRCh37)
Preferred name:: NC_000005.9:g.(?_176935330)_(176942071_?)del
HGVS:: NC_000005.9:g.(?_176935330)_(176942071_?)del
This HGVS expression did not pass validation

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003794982	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 22, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25920683, 33585199, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003794982

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 22, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Inherited and Somatic Defects in DDX41 in Myeloid Neoplasms.

Polprasert C, Schulze I, Sekeres MA, Makishima H, Przychodzen B, Hosono N, Singh J, Padgett RA, Gu X, Phillips JG, Clemente M, Parker Y, Lindner D, Dienes B, Jankowsky E, Saunthararajah Y, Du Y, Oakley K, Nguyen N, Mukherjee S, Pabst C, Godley LA, et al.

Cancer Cell. 2015 May 11;27(5):658-70. doi: 10.1016/j.ccell.2015.03.017. Epub 2015 Apr 23.

PubMed [citation]

PMID:: 25920683
PMCID:: PMC8713504

Next-Generation Sequencing of DDX41 in Myeloid Neoplasms Leads to Increased Detection of Germline Alterations.

Bannon SA, Routbort MJ, Montalban-Bravo G, Mehta RS, Jelloul FZ, Takahashi K, Daver N, Oran B, Pemmaraju N, Borthakur G, Naqvi K, Issa G, Sasaki K, Alvarado Y, Kadia TM, Konopleva M, Shamanna RK, Khoury JD, Ravandi F, Champlin R, Kantarjian HM, Bhalla K, et al.

Front Oncol. 2020;10:582213. doi: 10.3389/fonc.2020.582213.

PubMed [citation]

PMID:: 33585199
PMCID:: PMC7878971

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003794982.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 8-17 of the DDX41 gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. This variant has not been reported in the literature in individuals affected with DDX41-related conditions. This variant disrupts a region of the DDX41 protein in which other variant(s) (p.Ile396Thr) have been determined to be pathogenic (PMID: 25920683, 33585199; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 11, 2023

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