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NM_025132.4(WDR19):c.3533G>A (p.Arg1178Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(2);Pathogenic(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 27, 2020
Accession:
VCV000127158.6
Variation ID:
127158
Description:
single nucleotide variant
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NM_025132.4(WDR19):c.3533G>A (p.Arg1178Gln)

Allele ID
132656
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4p14
Genomic location
4: 39273029 (GRCh38) GRCh38 UCSC
4: 39274649 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q8NEZ3:p.Arg1178Gln
NC_000004.11:g.39274649G>A
NC_000004.12:g.39273029G>A
... more HGVS
Protein change
R1178Q, R1018Q
Other names
-
Canonical SPDI
NC_000004.12:39273028:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00016
Trans-Omics for Precision Medicine (TOPMed) 0.00022
The Genome Aggregation Database (gnomAD) 0.00013
The Genome Aggregation Database (gnomAD), exomes 0.00005
Exome Aggregation Consortium (ExAC) 0.00013
The Genome Aggregation Database (gnomAD) 0.00015
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00027
Links
ClinGen: CA151412
UniProtKB: Q8NEZ3#VAR_073678
OMIM: 608151.0010
dbSNP: rs79436363
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Apr 24, 2018 RCV000433622.1
Uncertain significance 2 criteria provided, single submitter Dec 30, 2017 RCV000115014.3
Pathogenic 1 criteria provided, single submitter Sep 27, 2020 RCV000653250.3
Uncertain significance 1 criteria provided, single submitter May 1, 2018 RCV000754960.2
Pathogenic 1 criteria provided, single submitter Dec 31, 2017 RCV000850617.1
Likely pathogenic 1 criteria provided, single submitter Jul 9, 2020 RCV001262101.1

Clinical features observed in individuals with this variant

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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
450 476

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(May 30, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000516765.3
Submitted: (Nov 28, 2017)
Evidence details
Comment:
The R1178Q variant in the WDR19 gene has been reported previously in the homozygous andcompound heterozygous states in patients with WDR19-related disorders (Halbritter et al., … (more)
Uncertain significance
(May 01, 2018)
criteria provided, single submitter
Method: research
None
(Autosomal recessive inheritance)
Allele origin: unknown
Rare Disease Group, Clinical Genetics,Karolinska Institutet
Accession: SCV000788386.1
Submitted: (May 31, 2018)
Evidence details
Pathogenic
(Apr 24, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000860737.1
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (3)
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Dec 30, 2017)
criteria provided, single submitter
Method: curation
Senior-Loken syndrome 8
Allele origin: unknown
Department of Genetics,Sultan Qaboos University Hospital, Oman
Accession: SCV000891658.1
Submitted: (Oct 25, 2018)
Evidence details
Publications
PubMed (1)
Pathogenic
(Dec 31, 2017)
criteria provided, single submitter
Method: clinical testing
Nephronophthisis 13
Senior-Loken syndrome 8
Allele origin: germline
Baylor Genetics
Accession: SCV000992850.1
Submitted: (Mar 14, 2019)
Evidence details
Publications
PubMed (3)
Likely pathogenic
(Jul 09, 2020)
criteria provided, single submitter
Method: clinical testing
Leber congenital amaurosis
(Autosomal recessive inheritance)
Allele origin: germline
Institute of Vision Research, Yonsei University College of Medicine
Accession: SCV001371860.1
Submitted: (Oct 28, 2020)
Evidence details
Publications
PubMed (1)
Pathogenic
(Sep 27, 2020)
criteria provided, single submitter
Method: clinical testing
Senior-Loken syndrome 8
Asphyxiating thoracic dystrophy 5
Allele origin: germline
Invitae
Accession: SCV000775126.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces arginine with glutamine at codon 1178 of the WDR19 protein (p.Arg1178Gln). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(Aug 01, 2013)
no assertion criteria provided
Method: literature only
SENIOR-LOKEN SYNDROME 8
Allele origin: germline
OMIM
Accession: SCV000148923.3
Submitted: (Apr 30, 2014)
Evidence details
Publications
PubMed (1)

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
Copy number variations and multiallelic variants in Korean patients with Leber congenital amaurosis. Surl D Molecular vision 2020 PMID: 32165824
Diversity of renal phenotypes in patients with WDR19 mutations: Two case reports. Yoshikawa T Nephrology (Carlton, Vic.) 2017 PMID: 28621010
Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. Zhang Q Scientific reports 2016 PMID: 27596865
Hepatorenal fibrocystic diseases in children. Park E Pediatric nephrology (Berlin, Germany) 2016 PMID: 26260382
Nephronophthisis 13: implications of its association with Caroli disease and altered intracellular localization of WDR19 in the kidney. Lee JM Pediatric nephrology (Berlin, Germany) 2015 PMID: 25726036
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=WDR19 - - - -

Text-mined citations for rs79436363...

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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 Nov 27, 2021