6-105323714-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_002726.5(PREP):c.1268G>A(p.Arg423Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,786 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_002726.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PREP | NM_002726.5 | c.1268G>A | p.Arg423Gln | missense_variant | Exon 10 of 15 | ENST00000652536.2 | NP_002717.3 | |
PREP | XM_011535925.4 | c.1268G>A | p.Arg423Gln | missense_variant | Exon 10 of 11 | XP_011534227.1 | ||
PREP | XM_005267044.4 | c.1268G>A | p.Arg423Gln | missense_variant | Exon 10 of 11 | XP_005267101.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PREP | ENST00000652536.2 | c.1268G>A | p.Arg423Gln | missense_variant | Exon 10 of 15 | NM_002726.5 | ENSP00000499089.1 | |||
PREP | ENST00000369110.8 | c.1070G>A | p.Arg357Gln | missense_variant | Exon 12 of 17 | 1 | ENSP00000358106.4 | |||
PREP | ENST00000448705.1 | c.53G>A | p.Arg18Gln | missense_variant | Exon 1 of 2 | 2 | ENSP00000401796.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251266Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135782
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461474Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727084
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1268G>A (p.R423Q) alteration is located in exon 10 (coding exon 10) of the PREP gene. This alteration results from a G to A substitution at nucleotide position 1268, causing the arginine (R) at amino acid position 423 to be replaced by a glutamine (Q). 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