7-142255189-T-A
Variant summary
Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM1PP3_Strong
The NM_001001317.5(PRSS58):c.302A>T(p.Asp101Val) variant causes a missense change. The variant allele was found at a frequency of 0.000026 in 1,614,050 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_001001317.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_pathogenic. The variant received 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRSS58 | ENST00000547058.6 | c.302A>T | p.Asp101Val | missense_variant | Exon 4 of 6 | 1 | NM_001001317.5 | ENSP00000447588.2 | ||
PRSS58 | ENST00000552471.1 | c.302A>T | p.Asp101Val | missense_variant | Exon 3 of 5 | 2 | ENSP00000446916.1 | |||
ENSG00000241881 | ENST00000486508.2 | n.254+6406T>A | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000123 AC: 31AN: 251238 AF XY: 0.0000810 show subpopulations
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461856Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 727232 show subpopulations
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.302A>T (p.D101V) alteration is located in exon 4 (coding exon 3) of the PRSS58 gene. This alteration results from a A to T substitution at nucleotide position 302, causing the aspartic acid (D) at amino acid position 101 to be replaced by a valine (V). 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