rs61751266
Variant summary
Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_020366.4(RPGRIP1):c.1107delA(p.Glu370AsnfsTer5) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000411 in 1,458,418 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. K369K) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_020366.4 frameshift
Scores
Clinical Significance
Conservation
Publications
- cone-rod dystrophy 13Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, G2P
- Leber congenital amaurosis 6Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- cone-rod dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Leber congenital amaurosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Pathogenic. The variant received 16 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020366.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RPGRIP1 | TSL:1 MANE Select | c.1107delA | p.Glu370AsnfsTer5 | frameshift | Exon 10 of 25 | ENSP00000382895.2 | Q96KN7-1 | ||
| RPGRIP1 | TSL:5 | c.1026delA | p.Glu343AsnfsTer5 | frameshift | Exon 9 of 24 | ENSP00000451219.1 | G3V3F7 | ||
| RPGRIP1 | TSL:5 | c.1026delA | p.Glu343AsnfsTer5 | frameshift | Exon 9 of 21 | ENSP00000450445.1 | G3V236 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD2 exomes AF: 0.00 AC: 0AN: 246030 AF XY: 0.00
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1458418Hom.: 0 Cov.: 28 AF XY: 0.00000551 AC XY: 4AN XY: 725500 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 31
ClinVar
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at