rs878853177
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP2PP3_ModeratePP5
The NM_001378452.1(ITPR1):c.6326A>G(p.Glu2109Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E2109Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001378452.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.6326A>G | p.Glu2109Gly | missense_variant | 49/62 | ENST00000649015.2 | NP_001365381.1 | |
ITPR1 | NM_001168272.2 | c.6281A>G | p.Glu2094Gly | missense_variant | 48/61 | NP_001161744.1 | ||
ITPR1 | NM_001099952.4 | c.6182A>G | p.Glu2061Gly | missense_variant | 46/59 | NP_001093422.2 | ||
ITPR1 | NM_002222.7 | c.6137A>G | p.Glu2046Gly | missense_variant | 45/58 | NP_002213.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.6326A>G | p.Glu2109Gly | missense_variant | 49/62 | NM_001378452.1 | ENSP00000497605 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Gillespie syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 18, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at