NM_001127671.2(LIFR):c.653dup (p.Glu219fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Sep 10, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000790750.3

Allele description [Variation Report for NM_001127671.2(LIFR):c.653dup (p.Glu219fs)]

NM_001127671.2(LIFR):c.653dup (p.Glu219fs)

Gene:
LIFR:LIF receptor subunit alpha [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
5p13.1
Genomic location:
Preferred name:
NM_001127671.2(LIFR):c.653dup (p.Glu219fs)
HGVS:
  • NC_000005.10:g.38511873dup
  • NG_011817.1:g.88533dup
  • NM_001127671.2:c.653dupMANE SELECT
  • NM_001364297.1:c.653dup
  • NM_001364298.1:c.653dup
  • NM_002310.6:c.653dup
  • NP_001121143.1:p.Glu219fs
  • NP_001351226.1:p.Glu219fs
  • NP_001351227.1:p.Glu219fs
  • NP_002301.1:p.Glu219fs
  • NC_000005.9:g.38511974_38511975insA
  • NC_000005.9:g.38511975dup
  • NM_001127671.1:c.653dup
  • NM_002310.5:c.653dup
Protein change:
E219fs
Links:
OMIM: 151443.0001; dbSNP: rs886042160
NCBI 1000 Genomes Browser:
rs886042160
Molecular consequence:
  • NM_001127671.2:c.653dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001364297.1:c.653dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001364298.1:c.653dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002310.6:c.653dup - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000332228EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Pathogenic
(Jun 19, 2015)
germlineclinical testing

Citation Link,

SCV001374288Invitaecriteria provided, single submitter
Pathogenic
(Sep 10, 2019)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Null leukemia inhibitory factor receptor (LIFR) mutations in Stuve-Wiedemann/Schwartz-Jampel type 2 syndrome.

Dagoneau N, Scheffer D, Huber C, Al-Gazali LI, Di Rocco M, Godard A, Martinovic J, Raas-Rothschild A, Sigaudy S, Unger S, Nicole S, Fontaine B, Taupin JL, Moreau JF, Superti-Furga A, Le Merrer M, Bonaventure J, Munnich A, Legeai-Mallet L, Cormier-Daire V.

Am J Hum Genet. 2004 Feb;74(2):298-305. Epub 2004 Jan 21.

PubMed [citation]
PMID:
14740318
PMCID:
PMC1181927

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 EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000332228.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV001374288.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Glu219Glyfs*3) in the LIFR gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in several individuals affected with Stuve-Wiedemann syndrome (PMID: 14740318). ClinVar contains an entry for this variant (Variation ID: 281444). Loss-of-function variants in LIFR are known to be pathogenic (PMID: 14740318). 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 8, 2021

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