6-30557379-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025263.4(PRR3):c.35C>T(p.Pro12Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,460,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025263.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRR3 | NM_025263.4 | c.35C>T | p.Pro12Leu | missense_variant | Exon 1 of 4 | ENST00000376560.8 | NP_079539.2 | |
PRR3 | NM_001077497.3 | c.35C>T | p.Pro12Leu | missense_variant | Exon 1 of 3 | NP_001070965.1 | ||
PRR3 | XM_047419381.1 | c.193C>T | p.His65Tyr | missense_variant | Exon 1 of 3 | XP_047275337.1 | ||
PRR3 | XM_047419382.1 | c.193C>T | p.His65Tyr | missense_variant | Exon 1 of 2 | XP_047275338.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 242386Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133116
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460400Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726496
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.35C>T (p.P12L) alteration is located in exon 1 (coding exon 1) of the PRR3 gene. This alteration results from a C to T substitution at nucleotide position 35, causing the proline (P) at amino acid position 12 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