rs1555474009
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_014714.4(IFT140):c.4239_4240insCTAC(p.Tyr1414LeufsTer48) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 33)
Consequence
IFT140
NM_014714.4 frameshift
NM_014714.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.80
Genes affected
IFT140 (HGNC:29077): (intraflagellar transport 140) This gene encodes one of the subunits of the intraflagellar transport (IFT) complex A. Intraflagellar transport is involved in the genesis, resorption and signaling of primary cilia. The primary cilium is a microtubule-based sensory organelle at the surface of most quiescent mammalian cells, that receives signals from its environment, such as the flow of fluid, light or odors, and transduces those signals to the nucleus. Loss of the corresponding protein in mouse results in renal cystic disease. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 4 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 16-1511093-A-AGTAG is Pathogenic according to our data. Variant chr16-1511093-A-AGTAG is described in ClinVar as [Pathogenic]. Clinvar id is 523182.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.4239_4240insCTAC | p.Tyr1414LeufsTer48 | frameshift_variant | 31/31 | ENST00000426508.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.4239_4240insCTAC | p.Tyr1414LeufsTer48 | frameshift_variant | 31/31 | 5 | NM_014714.4 | P1 | |
IFT140 | ENST00000361339.9 | c.1821_1822insCTAC | p.Tyr608LeufsTer48 | frameshift_variant | 13/13 | 1 | |||
IFT140 | ENST00000565298.5 | n.4063_4064insCTAC | non_coding_transcript_exon_variant | 19/19 | 2 | ||||
IFT140 | ENST00000397417.6 | c.*2677_*2678insCTAC | 3_prime_UTR_variant, NMD_transcript_variant | 24/24 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Retinal ciliopathy due to mutation in the retinitis pigmentosa-1 gene Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Laboratory of Medical Genetics (UMR_S 1112), INSERM/Strasbourg University | Jan 01, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at