rs139777154
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_016615.5(SLC6A13):c.1424G>T(p.Arg475Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000187 in 1,602,798 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. R475H) has been classified as Uncertain significance.
Frequency
Consequence
NM_016615.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A13 | NM_016615.5 | c.1424G>T | p.Arg475Leu | missense_variant | 13/15 | ENST00000343164.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A13 | ENST00000343164.9 | c.1424G>T | p.Arg475Leu | missense_variant | 13/15 | 1 | NM_016615.5 | P1 | |
SLC6A13 | ENST00000445055.6 | c.1148G>T | p.Arg383Leu | missense_variant | 11/13 | 2 | |||
SLC6A13 | ENST00000539668.1 | n.382G>T | non_coding_transcript_exon_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000422 AC: 1AN: 236832Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127602
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450666Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 720998
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at