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NM_018117.12(WDR11):c.3450T>G (p.Phe1150Leu) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Feb 1, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000059801.11

Allele description

NM_018117.12(WDR11):c.3450T>G (p.Phe1150Leu)

Gene:
WDR11:WD repeat domain 11 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q26.12
Genomic location:
Preferred name:
NM_018117.12(WDR11):c.3450T>G (p.Phe1150Leu)
HGVS:
  • NC_000010.11:g.120906788T>G
  • NG_023290.1:g.60614T>G
  • NM_018117.12:c.3450T>GMANE SELECT
  • NP_060587.8:p.Phe1150Leu
  • NC_000010.10:g.122666300T>G
  • NM_018117.11:c.3450T>G
  • Q9BZH6:p.Phe1150Leu
Protein change:
F1150L; PHE1150LEU
Links:
UniProtKB: Q9BZH6#VAR_069199; UniProtKB/Swiss-Prot: VAR_069199; OMIM: 606417.0001; dbSNP: rs139007744
NCBI 1000 Genomes Browser:
rs139007744
Molecular consequence:
  • NM_018117.12:c.3450T>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000091371UniProtKB/Swiss-Prot
no classification provided
not providednot providednot provided

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

SCV001001395Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Nov 16, 2023)
germlineclinical testing

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

SCV002525421GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Jun 27, 2023)
germlineclinical testing

Citation Link,

SCV004699447CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Feb 1, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providednot providednot providednot providednot providednot provided1not providedliterature only
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

WDR11, a WD protein that interacts with transcription factor EMX1, is mutated in idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

Kim HG, Ahn JW, Kurth I, Ullmann R, Kim HT, Kulharya A, Ha KS, Itokawa Y, Meliciani I, Wenzel W, Lee D, Rosenberger G, Ozata M, Bick DP, Sherins RJ, Nagase T, Tekin M, Kim SH, Kim CH, Ropers HH, Gusella JF, Kalscheuer V, et al.

Am J Hum Genet. 2010 Oct 8;87(4):465-79. doi: 10.1016/j.ajhg.2010.08.018.

PubMed [citation]
PMID:
20887964
PMCID:
PMC2948809

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From UniProtKB/Swiss-Prot, SCV000091371.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From Invitae, SCV001001395.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV002525421.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Published functional studies suggest that this variant results in a reduced capacity of the protein to enter the nucleus (Kim et al., 2018); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 29330225, 22035731, 25254043, 27828722, 34426522, 35432193, Patil2022[paper], 36517585, 29263200, 20887964)

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

From CeGaT Center for Human Genetics Tuebingen, SCV004699447.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

WDR11: PP3, PS3:Supporting, BS1, BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Mar 10, 2024