rs876657372
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_003619.4(PRSS12):c.1355_1358delACGT(p.Asp452AlafsTer50) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as no classifications from unflagged records (no stars). Synonymous variant affecting the same amino acid position (i.e. D452D) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_003619.4 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRSS12 | NM_003619.4 | c.1355_1358delACGT | p.Asp452AlafsTer50 | frameshift_variant | Exon 7 of 13 | ENST00000296498.3 | NP_003610.2 | |
PRSS12 | XM_011532387.3 | c.1355_1358delACGT | p.Asp452AlafsTer50 | frameshift_variant | Exon 7 of 9 | XP_011530689.1 | ||
PRSS12 | XM_005263318.5 | c.1355_1358delACGT | p.Asp452AlafsTer50 | frameshift_variant | Exon 7 of 10 | XP_005263375.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRSS12 | ENST00000296498.3 | c.1355_1358delACGT | p.Asp452AlafsTer50 | frameshift_variant | Exon 7 of 13 | 1 | NM_003619.4 | ENSP00000296498.3 | ||
PRSS12 | ENST00000503043.1 | n.383_386delACGT | non_coding_transcript_exon_variant | Exon 3 of 3 | 5 | |||||
PRSS12 | ENST00000515089.1 | n.-59_-56delACGT | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Intellectual disability, autosomal recessive 1 Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at