3-48466996-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_ModeratePP5_Moderate
The NM_033629.6(TREX1):c.341G>T(p.Arg114Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R114H) has been classified as Pathogenic.
Frequency
Consequence
NM_033629.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TREX1 | NM_033629.6 | c.341G>T | p.Arg114Leu | missense_variant | Exon 2 of 2 | ENST00000625293.3 | NP_338599.1 | |
ATRIP | NM_130384.3 | c.*1442G>T | 3_prime_UTR_variant | Exon 13 of 13 | ENST00000320211.10 | NP_569055.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TREX1 | ENST00000625293.3 | c.341G>T | p.Arg114Leu | missense_variant | Exon 2 of 2 | 6 | NM_033629.6 | ENSP00000486676.2 | ||
ATRIP | ENST00000320211.10 | c.*1442G>T | 3_prime_UTR_variant | Exon 13 of 13 | 1 | NM_130384.3 | ENSP00000323099.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1460932Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726832
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Aicardi-Goutieres syndrome 1 Pathogenic:1
Criteria applied: PM5_STR,PM2_SUP,PP3,PM3_SUP -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.