ClinVar Miner

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

dbSNP: rs1561159768
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001008588 SCV001168361 likely pathogenic not provided 2019-02-11 criteria provided, single submitter clinical testing 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.
Invitae RCV001008588 SCV002232942 pathogenic not provided 2022-09-23 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 817458). This variant has not been reported in the literature in individuals affected with LIFR-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Ile304Metfs*10) in the LIFR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LIFR are known to be pathogenic (PMID: 14740318).
Natera, Inc. RCV001276357 SCV001462557 likely pathogenic Stuve-Wiedemann syndrome 2020-09-16 no assertion criteria provided clinical testing

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