rs769032474
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_015459.5(ATL3):c.854T>G(p.Ile285Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,150 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. I285T) has been classified as Uncertain significance.
Frequency
Consequence
NM_015459.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATL3 | NM_015459.5 | c.854T>G | p.Ile285Ser | missense_variant | 9/13 | ENST00000398868.8 | |
ATL3 | NM_001290048.2 | c.800T>G | p.Ile267Ser | missense_variant | 9/13 | ||
ATL3 | XM_047426725.1 | c.1010T>G | p.Ile337Ser | missense_variant | 10/14 | ||
ATL3 | XM_006718493.2 | c.797T>G | p.Ile266Ser | missense_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATL3 | ENST00000398868.8 | c.854T>G | p.Ile285Ser | missense_variant | 9/13 | 1 | NM_015459.5 | ||
ATL3 | ENST00000538786.1 | c.800T>G | p.Ile267Ser | missense_variant | 9/13 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 30
GnomAD4 exome Cov.: 31
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at