rs104894475
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_152443.3(RDH12):c.451C>A(p.His151Asn) variant causes a missense, splice region 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. 1/1 splice prediction tools predict no significant impact on normal splicing. 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. H151D) has been classified as Pathogenic.
Frequency
Consequence
NM_152443.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDH12 | NM_152443.3 | c.451C>A | p.His151Asn | missense_variant, splice_region_variant | 7/9 | ENST00000551171.6 | |
RDH12 | XM_047430965.1 | c.451C>A | p.His151Asn | missense_variant, splice_region_variant | 7/9 | ||
GPHN | XM_047430879.1 | c.1313-8212C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.451C>A | p.His151Asn | missense_variant, splice_region_variant | 7/9 | 1 | NM_152443.3 | P1 | |
RDH12 | ENST00000267502.3 | c.451C>A | p.His151Asn | missense_variant, splice_region_variant | 6/8 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Leber congenital amaurosis 13 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2004 | - - |
Pathogenic, no assertion criteria provided | research | Laboratory of Genetics in Ophthalmology, Institut Imagine | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at