NM_003180.3:c.595G>T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_003180.3(SYT5):c.595G>T(p.Asp199Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000691 in 1,592,498 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_003180.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYT5 | NM_003180.3 | c.595G>T | p.Asp199Tyr | missense_variant | Exon 6 of 9 | ENST00000354308.8 | NP_003171.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000694 AC: 10AN: 1440368Hom.: 0 Cov.: 32 AF XY: 0.00000699 AC XY: 5AN XY: 715812
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.595G>T (p.D199Y) alteration is located in exon 6 (coding exon 5) of the SYT5 gene. This alteration results from a G to T substitution at nucleotide position 595, causing the aspartic acid (D) at amino acid position 199 to be replaced by a tyrosine (Y). 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