rs104894459
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3PP5
The NM_001354768.3(NRL):c.148T>A(p.Ser50Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S50L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001354768.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NRL | NM_001354768.3 | c.148T>A | p.Ser50Thr | missense_variant | 2/3 | ENST00000561028.6 | NP_001341697.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRL | ENST00000561028.6 | c.148T>A | p.Ser50Thr | missense_variant | 2/3 | 2 | NM_001354768.3 | ENSP00000454062.2 | ||
NRL | ENST00000396997.1 | c.148T>A | p.Ser50Thr | missense_variant | 3/4 | 1 | ENSP00000380193.1 | |||
NRL | ENST00000397002.6 | c.148T>A | p.Ser50Thr | missense_variant | 2/3 | 1 | ENSP00000380197.2 | |||
NRL | ENST00000558280.1 | c.148T>A | p.Ser50Thr | missense_variant | 3/3 | 5 | ENSP00000454180.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Retinitis pigmentosa 27 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at