rs1555794302
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_015629.4(PRPF31):c.1129delC(p.Arg377ValfsTer2) 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. R377R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_015629.4 frameshift
Scores
Clinical Significance
Conservation
Publications
- PRPF31-related retinopathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- retinitis pigmentosa 11Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- retinitis pigmentosaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Pathogenic. The variant received 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPF31 | NM_015629.4 | c.1129delC | p.Arg377ValfsTer2 | frameshift_variant | Exon 11 of 14 | ENST00000321030.9 | NP_056444.3 | |
PRPF31 | XM_006723137.5 | c.1129delC | p.Arg377ValfsTer2 | frameshift_variant | Exon 11 of 14 | XP_006723200.1 | ||
PRPF31 | XM_047438587.1 | c.*264delC | downstream_gene_variant | XP_047294543.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD4 exome Cov.: 43
GnomAD4 genome Cov.: 28
ClinVar
Submissions by phenotype
Retinitis pigmentosa Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at