NM_001127671.2(LIFR):c.912_915del (p.Ile304fs) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Feb 11, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001008588.1

Allele description [Variation Report for NM_001127671.2(LIFR):c.912_915del (p.Ile304fs)]

NM_001127671.2(LIFR):c.912_915del (p.Ile304fs)

Gene:
LIFR:LIF receptor subunit alpha [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5p13.1
Genomic location:
Preferred name:
NM_001127671.2(LIFR):c.912_915del (p.Ile304fs)
HGVS:
  • NC_000005.10:g.38510541_38510544del
  • NG_011817.1:g.89863_89866del
  • NM_001127671.2:c.912_915delMANE SELECT
  • NM_001364297.1:c.912_915del
  • NM_001364298.1:c.912_915del
  • NM_002310.6:c.912_915del
  • NP_001121143.1:p.Ile304fs
  • NP_001351226.1:p.Ile304fs
  • NP_001351227.1:p.Ile304fs
  • NP_002301.1:p.Ile304fs
  • NC_000005.9:g.38510643_38510646del
  • NM_002310.5:c.912_915delTTCT
  • NM_002310.6:c.912_915delTTCT
Protein change:
I304fs
Links:
dbSNP: rs1561159768
NCBI 1000 Genomes Browser:
rs1561159768
Molecular consequence:
  • NM_001127671.2:c.912_915del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001364297.1:c.912_915del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001364298.1:c.912_915del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002310.6:c.912_915del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001168361GeneDxcriteria provided, single submitter
Likely pathogenic
(Feb 11, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168361.1

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

Description

The c.912_915delTTCT variant in the LIFR gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.912_915delTTCT variant causes a frameshift starting with codon Isoleucine 304, changes this amino acid to a Methionine residue, and creates a premature Stop codon at position 10 of the new reading frame, denoted p.Ile304MetfsX10. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.912_915delTTCT variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.912_915delTTCT as a pathogenic variant.

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

Last Updated: Oct 8, 2021

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