ClinVar Miner

Submissions for variant NM_001102564.3(IFT43):c.100G>A (p.Glu34Lys)

gnomAD frequency: 0.00009  dbSNP: rs140366557
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
SIB Swiss Institute of Bioinformatics RCV000579001 SCV000883291 likely pathogenic Retinitis pigmentosa 81 2018-10-15 criteria provided, single submitter curation This variant is interpreted as Likely Pathogenic, for Retinitis pigmentosa 81, autosomal recessive. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS3-Moderate => PS3 downgraded in strength to Moderate (https://www.ncbi.nlm.nih.gov/pubmed/28973684). PP1-Moderate => PP1 upgraded in strength to Moderate (https://www.ncbi.nlm.nih.gov/pubmed/28973684).
Labcorp Genetics (formerly Invitae), Labcorp RCV001215266 SCV001387000 uncertain significance not provided 2022-10-04 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 34 of the IFT43 protein (p.Glu34Lys). This variant is present in population databases (rs140366557, gnomAD 0.05%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with autosomal recessive non-syndromic retinitis pigmentosa (PMID: 28973684). ClinVar contains an entry for this variant (Variation ID: 489395). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0". The lysine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Experimental studies have shown that this missense change affects IFT43 function (PMID: 28973684). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
OMIM RCV000579001 SCV000681406 pathogenic Retinitis pigmentosa 81 2019-08-09 no assertion criteria provided literature only

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