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

Clinical significance:Pathogenic (Last evaluated: Sep 27, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000653250.3

Allele description [Variation Report for NM_025132.4(WDR19):c.3533G>A (p.Arg1178Gln)]

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

Gene:
WDR19:WD repeat domain 19 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p14
Genomic location:
Preferred name:
NM_025132.4(WDR19):c.3533G>A (p.Arg1178Gln)
HGVS:
  • NC_000004.12:g.39273029G>A
  • NG_031813.1:g.95626G>A
  • NM_001317924.2:c.3053G>A
  • NM_025132.4:c.3533G>AMANE SELECT
  • NP_001304853.1:p.Arg1018Gln
  • NP_079408.3:p.Arg1178Gln
  • NC_000004.11:g.39274649G>A
  • NM_025132.3:c.3533G>A
  • Q8NEZ3:p.Arg1178Gln
Protein change:
R1018Q; ARG1178GLN
Links:
UniProtKB: Q8NEZ3#VAR_073678; OMIM: 608151.0010; dbSNP: rs79436363
NCBI 1000 Genomes Browser:
rs79436363
Molecular consequence:
  • NM_001317924.2:c.3053G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_025132.4:c.3533G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Asphyxiating thoracic dystrophy 5 (SRTD5)
Synonyms:
SHORT-RIB THORACIC DYSPLASIA 5 WITH OR WITHOUT POLYDACTYLY
Identifiers:
MONDO: MONDO:0013717; MedGen: C3280598; Orphanet: 474; OMIM: 614376
Name:
Senior-Loken syndrome 8 (SLSN8)
Identifiers:
MONDO: MONDO:0014579; MedGen: C4225376; Orphanet: 3156; OMIM: 616307

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000775126Invitaecriteria provided, single submitter
Pathogenic
(Sep 27, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy.

Halbritter J, Porath JD, Diaz KA, Braun DA, Kohl S, Chaki M, Allen SJ, Soliman NA, Hildebrandt F, Otto EA; GPN Study Group..

Hum Genet. 2013 Aug;132(8):865-84. doi: 10.1007/s00439-013-1297-0. Epub 2013 Apr 5.

PubMed [citation]
PMID:
23559409
PMCID:
PMC4643834

Diversity of renal phenotypes in patients with WDR19 mutations: Two case reports.

Yoshikawa T, Kamei K, Nagata H, Saida K, Sato M, Ogura M, Ito S, Miyazaki O, Urushihara M, Kondo S, Sugawara N, Ishizuka K, Hamasaki Y, Shishido S, Morisada N, Iijima K, Nagata M, Yoshioka T, Ogata K, Ishikura K.

Nephrology (Carlton). 2017 Jul;22(7):566-571. doi: 10.1111/nep.12996.

PubMed [citation]
PMID:
28621010
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000775126.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

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 small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs79436363, ExAC 0.06%). This variant has been reported in the literature in multiple individuals affected with nephronophthisis (PMID: 23559409, 25726036), cranioectodermal dysplasia (PMID: 28621010), and retinitis pigmentosa (PMID: 27596865). It has also been found to segregate with nephronophthisis in a single family (PMID: 25726036). ClinVar contains an entry for this variant (Variation ID: 127158). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: Tolerated; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 7, 2021

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