rs119103236
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_005787.6(ALG3):c.512G>T(p.Arg171Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,326 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. R171Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_005787.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG3 | NM_005787.6 | c.512G>T | p.Arg171Leu | missense_variant | 4/9 | ENST00000397676.8 | |
ALG3 | NM_001006941.2 | c.368G>T | p.Arg123Leu | missense_variant | 4/9 | ||
ALG3 | NR_024533.1 | n.443G>T | non_coding_transcript_exon_variant | 3/8 | |||
ALG3 | NR_024534.1 | n.506G>T | non_coding_transcript_exon_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG3 | ENST00000397676.8 | c.512G>T | p.Arg171Leu | missense_variant | 4/9 | 1 | NM_005787.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247844Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134586
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461326Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726920
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at