chr11-20626721-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_004211.5(SLC6A5):c.1274C>A(p.Thr425Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. T425M) has been classified as Uncertain significance.
Frequency
Consequence
NM_004211.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A5 | NM_004211.5 | c.1274C>A | p.Thr425Lys | missense_variant | 8/16 | ENST00000525748.6 | |
SLC6A5 | NM_001318369.2 | c.572C>A | p.Thr191Lys | missense_variant | 7/15 | ||
SLC6A5 | XM_017018544.3 | c.398C>A | p.Thr133Lys | missense_variant | 4/12 | ||
SLC6A5 | XR_007062528.1 | n.652C>A | non_coding_transcript_exon_variant | 5/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A5 | ENST00000525748.6 | c.1274C>A | p.Thr425Lys | missense_variant | 8/16 | 1 | NM_004211.5 | P1 | |
SLC6A5 | ENST00000298923.11 | c.*571C>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/15 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251080Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135696
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at