NM_145045.5(ODAD3):c.1256C>A (p.Ser419Ter) AND Primary ciliary dyskinesia 30

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 14, 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:: RCV000144450.14

Allele description [Variation Report for NM_145045.5(ODAD3):c.1256C>A (p.Ser419Ter)]

NM_145045.5(ODAD3):c.1256C>A (p.Ser419Ter)

Gene:

ODAD3:outer dynein arm docking complex subunit 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_145045.5(ODAD3):c.1256C>A (p.Ser419Ter)

HGVS:

NC_000019.10:g.11422722G>T
NG_041777.1:g.18061C>A
NM_001302453.1:c.1094C>A
NM_001302454.2:c.1076C>A
NM_145045.5:c.1256C>AMANE SELECT
NP_001289382.1:p.Ser365Ter
NP_001289383.1:p.Ser359Ter
NP_659482.3:p.Ser419Ter
NC_000019.9:g.11533390G>T
NM_145045.4:c.1256C>A

Protein change:

S359*; SER419TER

Links:

OMIM: 615956.0002; dbSNP: rs587777780

NCBI 1000 Genomes Browser:

rs587777780

Molecular consequence:

NM_001302453.1:c.1094C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001302454.2:c.1076C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_145045.5:c.1256C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Primary ciliary dyskinesia 30
Synonyms:: CILIARY DYSKINESIA, PRIMARY, 30, WITH OR WITHOUT SITUS INVERSUS
Identifiers:: MONDO: MONDO:0014465; MedGen: C4015016; Orphanet: 244; OMIM: 616037

Recent activity

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ankyrin repeat domain-containing protein 29 isoform X5 [Homo sapiens]
ankyrin repeat domain-containing protein 29 isoform X5 [Homo sapiens]
gi|2217316175|ref|XP_047293260.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000189517	OMIM	no assertion criteria provided	Pathogenic (Sep 4, 2014)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV003443113	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 14, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25192045, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000189517

OMIM

no assertion criteria provided

Pathogenic
(Sep 4, 2014)

germline

literature only

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

SCV003443113

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 14, 2023)

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
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

CCDC151 mutations cause primary ciliary dyskinesia by disruption of the outer dynein arm docking complex formation.

Hjeij R, Onoufriadis A, Watson CM, Slagle CE, Klena NT, Dougherty GW, Kurkowiak M, Loges NT, Diggle CP, Morante NF, Gabriel GC, Lemke KL, Li Y, Pennekamp P, Menchen T, Konert F, Marthin JK, Mans DA, Letteboer SJ, Werner C, Burgoyne T, Westermann C, et al.

Am J Hum Genet. 2014 Sep 4;95(3):257-74. doi: 10.1016/j.ajhg.2014.08.005.

PubMed [citation]

PMID:: 25192045
PMCID:: PMC4157146

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From OMIM, SCV000189517.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a 12-year-old boy, born of consanguineous Pakistani parents, with CILD30 (616037) and situs inversus, Hjeij et al. (2014) identified a homozygous c.1256C-A transversion in the CCDC151 gene, resulting in a ser419-to-ter (S419X) substitution. The mutation, which was found by a combination of linkage analysis and exome sequencing, segregated with the disorder in the family and was not found in the 1000 Genomes Project or Exome Variant Server databases.

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

From Invitae, SCV003443113.2

#	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 creates a premature translational stop signal (p.Ser419*) in the CCDC151 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CCDC151 are known to be pathogenic (PMID: 25192045). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with primary ciliary dyskinesia (PMID: 25192045). ClinVar contains an entry for this variant (Variation ID: 156366). 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: Jul 7, 2024

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