6-30558156-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025263.4(PRR3):c.113C>T(p.Pro38Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000348 in 1,612,784 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025263.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRR3 | NM_025263.4 | c.113C>T | p.Pro38Leu | missense_variant | Exon 2 of 4 | ENST00000376560.8 | NP_079539.2 | |
PRR3 | XM_047419381.1 | c.271C>T | p.Pro91Ser | missense_variant | Exon 2 of 3 | XP_047275337.1 | ||
PRR3 | NM_001077497.3 | c.106+706C>T | intron_variant | Intron 1 of 2 | NP_001070965.1 | |||
PRR3 | XM_047419382.1 | c.264+706C>T | intron_variant | Intron 1 of 1 | XP_047275338.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 29AN: 244676Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 133912
GnomAD4 exome AF: 0.000373 AC: 545AN: 1460612Hom.: 0 Cov.: 30 AF XY: 0.000388 AC XY: 282AN XY: 726612
GnomAD4 genome AF: 0.000112 AC: 17AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.113C>T (p.P38L) alteration is located in exon 2 (coding exon 2) of the PRR3 gene. This alteration results from a C to T substitution at nucleotide position 113, causing the proline (P) at amino acid position 38 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