6-105328904-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_002726.5(PREP):c.1138G>A(p.Gly380Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,614,034 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002726.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PREP | NM_002726.5 | c.1138G>A | p.Gly380Ser | missense_variant | Exon 9 of 15 | ENST00000652536.2 | NP_002717.3 | |
PREP | XM_011535925.4 | c.1138G>A | p.Gly380Ser | missense_variant | Exon 9 of 11 | XP_011534227.1 | ||
PREP | XM_005267044.4 | c.1138G>A | p.Gly380Ser | missense_variant | Exon 9 of 11 | XP_005267101.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PREP | ENST00000652536.2 | c.1138G>A | p.Gly380Ser | missense_variant | Exon 9 of 15 | NM_002726.5 | ENSP00000499089.1 | |||
PREP | ENST00000369110.8 | c.940G>A | p.Gly314Ser | missense_variant | Exon 11 of 17 | 1 | ENSP00000358106.4 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251388Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135856
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461886Hom.: 1 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727246
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1138G>A (p.G380S) alteration is located in exon 9 (coding exon 9) of the PREP gene. This alteration results from a G to A substitution at nucleotide position 1138, causing the glycine (G) at amino acid position 380 to be replaced by a serine (S). 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