rs140601882
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_005629.4(SLC6A8):c.1626C>A(p.Tyr542Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. 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 Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Y542Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005629.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.1626C>A | p.Tyr542Ter | stop_gained | 12/13 | ENST00000253122.10 | |
SLC6A8 | NM_001142805.2 | c.1596C>A | p.Tyr532Ter | stop_gained | 12/13 | ||
SLC6A8 | NM_001142806.1 | c.1281C>A | p.Tyr427Ter | stop_gained | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.1626C>A | p.Tyr542Ter | stop_gained | 12/13 | 1 | NM_005629.4 | P1 | |
SLC6A8 | ENST00000430077.6 | c.1281C>A | p.Tyr427Ter | stop_gained | 12/13 | 2 | |||
SLC6A8 | ENST00000485324.1 | n.1933C>A | non_coding_transcript_exon_variant | 5/6 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD4 exome Cov.: 38
GnomAD4 genome ? Cov.: 25
ClinVar
Submissions by phenotype
Creatine transporter deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 01, 2019 | This variant was identified as de novo. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at