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NM_025132.4(WDR19):c.781dup (p.Thr261fs)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 8, 2019
Accession:
VCV000446634.6
Variation ID:
446634
Description:
1bp duplication
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NM_025132.4(WDR19):c.781dup (p.Thr261fs)

Allele ID
440088
Variant type
Duplication
Variant length
1 bp
Cytogenetic location
4p14
Genomic location
4: 39205626-39205627 (GRCh38) GRCh38 UCSC
4: 39207246-39207247 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.39207247dup
NC_000004.12:g.39205627dup
NM_025132.4:c.781dup MANE Select NP_079408.3:p.Thr261fs frameshift
... more HGVS
Protein change
T101fs, T261fs
Other names
-
Canonical SPDI
NC_000004.12:39205626:A:AA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00009
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00004
Links
ClinGen: CA2891700
dbSNP: rs748656635
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
WDR19-Related Disorders
Uncertain significance 1 criteria provided, single submitter Jan 16, 2018 RCV000779441.1
Pathogenic 1 criteria provided, single submitter Dec 31, 2017 RCV000850616.1
Pathogenic 1 criteria provided, single submitter Aug 8, 2019 RCV001231474.2
Pathogenic/Likely pathogenic 2 no assertion criteria provided Jun 1, 2017 RCV000515920.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WDR19 - - GRCh38
GRCh37
427 453

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 16, 2018)
criteria provided, single submitter
Method: clinical testing
WDR19-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000916061.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (3)
Comment:
The WDR19 c.781dupA (p.Thr261AsnfsTer13) frameshift variant has been reported in three studies, where it was found in a compound heterozygous state with a missense variant … (more)
Pathogenic
(Dec 31, 2017)
criteria provided, single submitter
Method: clinical testing
Nephronophthisis 13
Senior-Loken syndrome 8
Allele origin: germline
Baylor Genetics
Accession: SCV000992849.1
Submitted: (Mar 14, 2019)
Evidence details
Publications
PubMed (2)
Pathogenic
(Aug 08, 2019)
criteria provided, single submitter
Method: clinical testing
Senior-Loken syndrome 8
Asphyxiating thoracic dystrophy 5
Allele origin: germline
Invitae
Accession: SCV001403998.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change creates a premature translational stop signal (p.Thr261Asnfs*13) in the WDR19 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Jun 01, 2017)
no assertion criteria provided
Method: research
Asphyxiating thoracic dystrophy
Allele origin: paternal
Dan Cohn Lab,University Of California Los Angeles
Accession: SCV000612046.1
Submitted: (Sep 01, 2017)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(-)
no assertion criteria provided
Method: research
asphyxiating thoracic dystrophy
Allele origin: inherited
University of Washington Center for Mendelian Genomics, University of Washington
Accession: SCV001479399.1
Submitted: (Nov 16, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Expanding the genetic architecture and phenotypic spectrum in the skeletal ciliopathies. Zhang W Human mutation 2018 PMID: 29068549
Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. Meng L JAMA pediatrics 2017 PMID: 28973083
Next-generation sequencing for diagnosis of rare diseases in the neonatal intensive care unit. Daoud H CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne 2016 PMID: 27241786
Reproductive genetic counseling challenges associated with diagnostic exome sequencing in a large academic private reproductive genetic counseling practice. Westerfield LE Prenatal diagnosis 2015 PMID: 26275793
WDR19: an ancient, retrograde, intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa and in Senior-Loken syndrome. Coussa RG Clinical genetics 2013 PMID: 23683095
Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy. Halbritter J Human genetics 2013 PMID: 23559409
Ciliopathies with skeletal anomalies and renal insufficiency due to mutations in the IFT-A gene WDR19. Bredrup C American journal of human genetics 2011 PMID: 22019273

Text-mined citations for rs748656635...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 10, 2021