chr2-44320424-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000341.4(SLC3A1):c.1843C>T(p.Pro615Ser) variant causes a missense change. 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. P615T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000341.4 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 |
---|---|---|---|---|---|---|---|
SLC3A1 | NM_000341.4 | c.1843C>T | p.Pro615Ser | missense_variant | 10/10 | ENST00000260649.11 | |
PREPL | NM_001171613.2 | c.*932G>A | 3_prime_UTR_variant | 14/14 | ENST00000409411.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A1 | ENST00000260649.11 | c.1843C>T | p.Pro615Ser | missense_variant | 10/10 | 1 | NM_000341.4 | P1 | |
PREPL | ENST00000409411.6 | c.*932G>A | 3_prime_UTR_variant | 14/14 | 1 | NM_001171613.2 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249682Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135050
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at