1-109477831-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001040709.2(SYPL2):c.470C>T(p.Thr157Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000373 in 1,608,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040709.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYPL2 | NM_001040709.2 | c.470C>T | p.Thr157Ile | missense_variant | Exon 5 of 6 | ENST00000369872.4 | NP_001035799.1 | |
SYPL2 | XM_011541283.3 | c.470C>T | p.Thr157Ile | missense_variant | Exon 5 of 7 | XP_011539585.1 | ||
SYPL2 | XM_011541284.3 | c.456+854C>T | intron_variant | Intron 4 of 5 | XP_011539586.1 | |||
SYPL2 | XM_011541285.2 | c.456+854C>T | intron_variant | Intron 4 of 4 | XP_011539587.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152246Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456610Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 724010
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.470C>T (p.T157I) alteration is located in exon 5 (coding exon 5) of the SYPL2 gene. This alteration results from a C to T substitution at nucleotide position 470, causing the threonine (T) at amino acid position 157 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at