NM_016516.3:c.2321C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016516.3(VPS54):c.2321C>T(p.Ser774Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,312 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016516.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS54 | ENST00000272322.9 | c.2321C>T | p.Ser774Leu | missense_variant | Exon 17 of 23 | 5 | NM_016516.3 | ENSP00000272322.4 | ||
VPS54 | ENST00000409558.8 | c.2285C>T | p.Ser762Leu | missense_variant | Exon 17 of 23 | 1 | ENSP00000386980.3 | |||
VPS54 | ENST00000354504.7 | c.1862C>T | p.Ser621Leu | missense_variant | Exon 14 of 20 | 1 | ENSP00000346499.3 | |||
VPS54 | ENST00000416400.1 | n.203C>T | non_coding_transcript_exon_variant | Exon 3 of 10 | 1 | ENSP00000414725.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460312Hom.: 0 Cov.: 29 AF XY: 0.00000551 AC XY: 4AN XY: 726440
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2321C>T (p.S774L) alteration is located in exon 17 (coding exon 16) of the VPS54 gene. This alteration results from a C to T substitution at nucleotide position 2321, causing the serine (S) at amino acid position 774 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.