NM_018139.3(DNAAF2):c.1156_1159dup (p.Glu387fs) AND Primary ciliary dyskinesia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 19, 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:: RCV000471836.7

Allele description [Variation Report for NM_018139.3(DNAAF2):c.1156_1159dup (p.Glu387fs)]

NM_018139.3(DNAAF2):c.1156_1159dup (p.Glu387fs)

Genes:

LOC130055542:ATAC-STARR-seq lymphoblastoid silent region 5699 [Gene]
DNAAF2:dynein axonemal assembly factor 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

14q21.3

Genomic location:

Preferred name:

NM_018139.3(DNAAF2):c.1156_1159dup (p.Glu387fs)

HGVS:

NC_000014.9:g.49633992_49633995dup
NG_013070.1:g.6237_6240dup
NM_001083908.2:c.1156_1159dup
NM_018139.3:c.1156_1159dupMANE SELECT
NP_001077377.1:p.Glu387fs
NP_060609.2:p.Glu387fs
NC_000014.8:g.50100708_50100709insCCCC
NC_000014.8:g.50100710_50100713dup
NM_018139.2:c.1156_1159dup
NM_018139.2:c.1156_1159dupGGGG

Protein change:

E387fs

Links:

dbSNP: rs902156961

NCBI 1000 Genomes Browser:

rs902156961

Molecular consequence:

NM_001083908.2:c.1156_1159dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_018139.3:c.1156_1159dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Primary ciliary dyskinesia
Synonyms:: 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
SCV000552216	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 19, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19052621, 24498942, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000552216

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 19, 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

Ktu/PF13 is required for cytoplasmic pre-assembly of axonemal dyneins.

Omran H, Kobayashi D, Olbrich H, Tsukahara T, Loges NT, Hagiwara H, Zhang Q, Leblond G, O'Toole E, Hara C, Mizuno H, Kawano H, Fliegauf M, Yagi T, Koshida S, Miyawaki A, Zentgraf H, Seithe H, Reinhardt R, Watanabe Y, Kamiya R, Mitchell DR, et al.

Nature. 2008 Dec 4;456(7222):611-6. doi: 10.1038/nature07471.

PubMed [citation]

PMID:: 19052621
PMCID:: PMC3279746

The role of molecular genetic analysis in the diagnosis of primary ciliary dyskinesia.

Kim RH, A Hall D, Cutz E, Knowles MR, Nelligan KA, Nykamp K, Zariwala MA, Dell SD.

Ann Am Thorac Soc. 2014 Mar;11(3):351-9. doi: 10.1513/AnnalsATS.201306-194OC.

PubMed [citation]

PMID:: 24498942
PMCID:: PMC4028737

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000552216.5

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 411172). This variant has not been reported in the literature in individuals affected with DNAAF2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.03%). This sequence change creates a premature translational stop signal (p.Glu387Glyfs*105) in the DNAAF2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DNAAF2 are known to be pathogenic (PMID: 19052621, 24498942).

#	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 15, 2024

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