NM_181426.2(CCDC39):c.2497_2498del (p.Gln833fs) AND Primary ciliary dyskinesia

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 16, 2017
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:: RCV000529219.2

Allele description

NM_181426.2(CCDC39):c.2497_2498del (p.Gln833fs)

Genes:

CCDC39:coiled-coil domain containing 39 [Gene - OMIM - HGNC]
TTC14:tetratricopeptide repeat domain 14 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q26.33

Genomic location:

Preferred name:

NM_181426.2(CCDC39):c.2497_2498del (p.Gln833fs)

HGVS:

NC_000003.12:g.180616605_180616606del
NG_029581.1:g.67891_67892del
NM_001288582.2:c.1775-775_1775-774del
NM_181426.2:c.2497_2498delMANE SELECT
NP_852091.1:p.Gln833fs
NC_000003.11:g.180334393_180334394del
NM_181426.1:c.2497_2498delCA

Protein change:

Q833fs

Links:

dbSNP: rs1007345781

NCBI 1000 Genomes Browser:

rs1007345781

Molecular consequence:

NM_181426.2:c.2497_2498del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001288582.2:c.1775-775_1775-774del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Primary ciliary dyskinesia (PCD)
Synonyms:: Polynesian bronchiectasis; Immotile cilia syndrome; Ciliary dyskinesia
Identifiers:: MONDO: MONDO:0016575; MedGen: C0008780; OMIM: PS244400; Human Phenotype Ontology: HP:0012265

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000624546	Invitae	criteria provided, single submitter (Nykamp K et al. (Genet Med 2017))	Pathogenic (Oct 16, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23891469, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000624546

Invitae

criteria provided, single submitter

(Nykamp K et al. (Genet Med 2017))

Pathogenic
(Oct 16, 2017)

germline

clinical testing

PubMed (2)
[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

ZMYND10 is mutated in primary ciliary dyskinesia and interacts with LRRC6.

Zariwala MA, Gee HY, Kurkowiak M, Al-Mutairi DA, Leigh MW, Hurd TW, Hjeij R, Dell SD, Chaki M, Dougherty GW, Adan M, Spear PC, Esteve-Rudd J, Loges NT, Rosenfeld M, Diaz KA, Olbrich H, Wolf WE, Sheridan E, Batten TF, Halbritter J, Porath JD, et al.

Am J Hum Genet. 2013 Aug 8;93(2):336-45. doi: 10.1016/j.ajhg.2013.06.007. Epub 2013 Jul 25.

PubMed [citation]

PMID:: 23891469
PMCID:: PMC3738827

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000624546.2

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

Description

This sequence change deletes 2 nucleotides from exon 18 of the CCDC39 mRNA (c.2497_2498delCA), causing a frameshift at codon 833. This creates a premature translational stop signal (p.Gln833Valfs*6) and is expected to result in an absent or disrupted protein product. Loss-of-function variants in CCDC39 are known to be pathogenic. This particular variant has been reported in the literature in a family affected with primary ciliary dyskinesia (PMID: 23891469). 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: Apr 18, 2020

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