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NM_025132.4(WDR19):c.2129T>C (p.Leu710Ser)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Apr 26, 2021)
Last evaluated:
Apr 8, 2021
Accession:
VCV000030703.5
Variation ID:
30703
Description:
single nucleotide variant
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NM_025132.4(WDR19):c.2129T>C (p.Leu710Ser)

Allele ID
39660
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4p14
Genomic location
4: 39231943 (GRCh38) GRCh38 UCSC
4: 39233563 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.39233563T>C
NC_000004.12:g.39231943T>C
NM_025132.4:c.2129T>C MANE Select NP_079408.3:p.Leu710Ser missense
... more HGVS
Protein change
L710S, L550S
Other names
-
Canonical SPDI
NC_000004.12:39231942:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA199262
UniProtKB: Q8NEZ3#VAR_067314
OMIM: 608151.0001
dbSNP: rs387906980
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, single submitter Apr 8, 2021 RCV000169775.5
Pathogenic 1 criteria provided, single submitter May 28, 2019 RCV000987440.1
Pathogenic 1 criteria provided, single submitter Jul 30, 2020 RCV001047050.2
Pathogenic 2 no assertion criteria provided Sep 12, 2013 RCV000023681.6
Likely pathogenic 1 no assertion criteria provided - RCV001356848.1
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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
419 445

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Asphyxiating thoracic dystrophy 5
Allele origin: unknown
Mendelics
Accession: SCV001136730.1
Submitted: (Oct 22, 2019)
Evidence details
Pathogenic
(Jul 30, 2020)
criteria provided, single submitter
Method: clinical testing
Senior-Loken syndrome 8
Asphyxiating thoracic dystrophy 5
Allele origin: germline
Invitae
Accession: SCV001210982.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces leucine with serine at codon 710 of the WDR19 protein (p.Leu710Ser). The leucine residue is highly conserved and there is a … (more)
Pathogenic
(Apr 08, 2021)
criteria provided, single submitter
Method: research
Senior-Loken syndrome 8
Allele origin: germline
Ocular Genomics Institute, Massachusetts Eye and Ear
Accession: SCV001573264.1
Submitted: (Apr 26, 2021)
Evidence details
Publications
PubMed (4)
Comment:
The WDR19 c.2129T>C variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we … (more)
pathologic
(Sep 12, 2013)
no assertion criteria provided
Method: curation
Cranioectodermal Dysplasia
Allele origin: not provided
GeneReviews
Accession: SCV000087013.1
Submitted: (Apr 30, 2013)
Evidence details
Comment:
Converted during submission to Pathogenic.
Pathogenic
(Aug 01, 2013)
no assertion criteria provided
Method: literature only
CRANIOECTODERMAL DYSPLASIA 4 (1 family)
Allele origin: germline
OMIM
Accession: SCV000044972.5
Submitted: (Apr 10, 2015)
Evidence details
Publications
PubMed (2)
Pathogenic
(Aug 01, 2013)
no assertion criteria provided
Method: literature only
SENIOR-LOKEN SYNDROME 8
Allele origin: germline
OMIM
Accession: SCV000221337.3
Submitted: (Apr 10, 2015)
Evidence details
Publications
PubMed (2)
Likely pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001552119.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The WDR19 p.L710S variant was identified in the literature as a homozygous variant in 2 of 151 families (freq=0.013) with autosomal recessive Retinitis Pigmentosa from … (more)

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
Cranioectodermal Dysplasia Tan W - 2021 PMID: 24027799
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
Mechanistic Evidence in Evidence-Based Medicine: A Conceptual Framework Goodman SN - 2013 PMID: 24027800
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
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 rs387906980...

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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