NM_001378452.1:c.6349G>A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP2PP3
The NM_001378452.1(ITPR1):c.6349G>A(p.Ala2117Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A2117S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378452.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.6349G>A | p.Ala2117Thr | missense_variant | Exon 49 of 62 | ENST00000649015.2 | NP_001365381.1 | |
ITPR1 | NM_001168272.2 | c.6304G>A | p.Ala2102Thr | missense_variant | Exon 48 of 61 | NP_001161744.1 | ||
ITPR1 | NM_001099952.4 | c.6205G>A | p.Ala2069Thr | missense_variant | Exon 46 of 59 | NP_001093422.2 | ||
ITPR1 | NM_002222.7 | c.6160G>A | p.Ala2054Thr | missense_variant | Exon 45 of 58 | NP_002213.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.6349G>A | p.Ala2117Thr | missense_variant | Exon 49 of 62 | NM_001378452.1 | ENSP00000497605.1 | |||
ITPR1 | ENST00000354582.12 | c.6325G>A | p.Ala2109Thr | missense_variant | Exon 49 of 62 | 5 | ENSP00000346595.8 | |||
ITPR1 | ENST00000648266.1 | c.6322G>A | p.Ala2108Thr | missense_variant | Exon 49 of 62 | ENSP00000498014.1 | ||||
ITPR1 | ENST00000650294.1 | c.6307G>A | p.Ala2103Thr | missense_variant | Exon 48 of 61 | ENSP00000498056.1 | ||||
ITPR1 | ENST00000443694.5 | c.6304G>A | p.Ala2102Thr | missense_variant | Exon 48 of 61 | 1 | ENSP00000401671.2 | |||
ITPR1 | ENST00000648309.1 | c.6277G>A | p.Ala2093Thr | missense_variant | Exon 46 of 59 | ENSP00000497026.1 | ||||
ITPR1 | ENST00000357086.10 | c.6205G>A | p.Ala2069Thr | missense_variant | Exon 46 of 59 | 1 | ENSP00000349597.4 | |||
ITPR1 | ENST00000456211.8 | c.6160G>A | p.Ala2054Thr | missense_variant | Exon 45 of 58 | 1 | ENSP00000397885.2 | |||
ITPR1 | ENST00000648038.1 | c.4111G>A | p.Ala1371Thr | missense_variant | Exon 29 of 42 | ENSP00000497872.1 | ||||
ITPR1 | ENST00000648431.1 | c.3649G>A | p.Ala1217Thr | missense_variant | Exon 27 of 39 | ENSP00000498149.1 | ||||
ITPR1 | ENST00000648212.1 | c.3256G>A | p.Ala1086Thr | missense_variant | Exon 25 of 39 | ENSP00000498022.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152122Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1459922Hom.: 0 Cov.: 29 AF XY: 0.00000551 AC XY: 4AN XY: 726322
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152122Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at