rs750473506
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP2PP3_ModeratePP5
The NM_001378452.1(ITPR1):āc.2683A>Gā(p.Ile895Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001378452.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.2683A>G | p.Ile895Val | missense_variant | 23/62 | ENST00000649015.2 | |
ITPR1 | NM_001168272.2 | c.2638A>G | p.Ile880Val | missense_variant | 22/61 | ||
ITPR1 | NM_001099952.4 | c.2683A>G | p.Ile895Val | missense_variant | 23/59 | ||
ITPR1 | NM_002222.7 | c.2638A>G | p.Ile880Val | missense_variant | 22/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.2683A>G | p.Ile895Val | missense_variant | 23/62 | NM_001378452.1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248414Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134814
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458030Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 725562
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 27, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 22, 2018 | - - |
Spastic ataxia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris | Jul 12, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at