rs1555793207
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_015629.4(PRPF31):c.838_841dup(p.Gln281ArgfsTer44) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. I279I) has been classified as Uncertain significance. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
PRPF31
NM_015629.4 frameshift
NM_015629.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.981
Genes affected
PRPF31 (HGNC:15446): (pre-mRNA processing factor 31) This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 19-54124637-T-TCGTG is Pathogenic according to our data. Variant chr19-54124637-T-TCGTG is described in ClinVar as [Likely_pathogenic]. Clinvar id is 438046.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRPF31 | NM_015629.4 | c.838_841dup | p.Gln281ArgfsTer44 | frameshift_variant | 8/14 | ENST00000321030.9 | |
PRPF31-AS1 | XR_007067340.1 | n.88-1048_88-1047insCACG | intron_variant, non_coding_transcript_variant | ||||
PRPF31 | XM_006723137.5 | c.838_841dup | p.Gln281ArgfsTer44 | frameshift_variant | 8/14 | ||
PRPF31 | XM_047438587.1 | c.838_841dup | p.Gln281ArgfsTer51 | frameshift_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPF31 | ENST00000321030.9 | c.838_841dup | p.Gln281ArgfsTer44 | frameshift_variant | 8/14 | 1 | NM_015629.4 | P1 | |
PRPF31-AS1 | ENST00000452097.1 | n.706_707insCACG | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Retinitis pigmentosa Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | Jan 01, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at