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NM_181426.2(CCDC39):c.1871_1872del (p.Ile624fs) AND CCDC39-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 28, 2023
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:
RCV003420209.4

Allele description [Variation Report for NM_181426.2(CCDC39):c.1871_1872del (p.Ile624fs)]

NM_181426.2(CCDC39):c.1871_1872del (p.Ile624fs)

Gene:
CCDC39:coiled-coil domain 39 molecular ruler complex subunit [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3q26.33
Genomic location:
Preferred name:
NM_181426.2(CCDC39):c.1871_1872del (p.Ile624fs)
HGVS:
  • NC_000003.12:g.180641996_180641997del
  • NG_029581.1:g.42500_42501del
  • NM_181426.2:c.1871_1872delMANE SELECT
  • NP_852091.1:p.Ile624fs
  • NC_000003.11:g.180359783_180359784del
  • NC_000003.11:g.180359784_180359785del
  • NM_181426.1:c.1871_1872delTA
  • NM_181426.2:c.1871_1872delTAMANE SELECT
Protein change:
I624fs
Links:
dbSNP: rs1560086701
NCBI 1000 Genomes Browser:
rs1560086701
Molecular consequence:
  • NM_181426.2:c.1871_1872del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
CCDC39-related disorder
Synonyms:
CCDC39-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004116367PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Feb 28, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 PreventionGenetics, part of Exact Sciences, SCV004116367.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The CCDC39 c.1871_1872delTA variant is predicted to result in a frameshift and premature protein termination (p.Ile624Lysfs*3). This variant has been reported in the homozygous state in multiple individuals with Primary ciliary dyskinesia (Monies et al. 2019. PubMed ID: 31130284. Table S1; Fassad et al. 2019. PubMed ID: 31879361). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Frameshift variants in CCDC39 are expected to be pathogenic. This variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024