X-7077407-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_012080.5(PUDP):c.323C>T(p.Pro108Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,208,992 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012080.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PUDP | NM_012080.5 | c.323C>T | p.Pro108Leu | missense_variant | 3/4 | ENST00000381077.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PUDP | ENST00000381077.10 | c.323C>T | p.Pro108Leu | missense_variant | 3/4 | 1 | NM_012080.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000899 AC: 1AN: 111291Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33481
GnomAD3 exomes AF: 0.0000166 AC: 3AN: 180900Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 66912
GnomAD4 exome AF: 0.0000191 AC: 21AN: 1097701Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 7AN XY: 363135
GnomAD4 genome ? AF: 0.00000899 AC: 1AN: 111291Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33481
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.392C>T (p.P131L) alteration is located in exon 4 (coding exon 4) of the PUDP gene. This alteration results from a C to T substitution at nucleotide position 392, causing the proline (P) at amino acid position 131 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