rs104894474
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_152443.3(RDH12):c.379G>T(p.Gly127Ter) variant causes a stop gained 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 (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
RDH12
NM_152443.3 stop_gained
NM_152443.3 stop_gained
Scores
5
1
1
Clinical Significance
Conservation
PhyloP100: 10.0
Genes affected
RDH12 (HGNC:19977): (retinol dehydrogenase 12) The protein encoded by this gene is an NADPH-dependent retinal reductase whose highest activity is toward 9-cis and all-trans-retinol. The encoded enzyme also plays a role in the metabolism of short-chain aldehydes but does not exhibit steroid dehydrogenase activity. Defects in this gene are a cause of Leber congenital amaurosis type 13 and Retinitis Pigmentosa 53. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 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 14-67726086-G-T is Pathogenic according to our data. Variant chr14-67726086-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 2051.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-67726086-G-T is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDH12 | NM_152443.3 | c.379G>T | p.Gly127Ter | stop_gained | 6/9 | ENST00000551171.6 | |
RDH12 | XM_047430965.1 | c.379G>T | p.Gly127Ter | stop_gained | 6/9 | ||
GPHN | XM_047430879.1 | c.1313-9109G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.379G>T | p.Gly127Ter | stop_gained | 6/9 | 1 | NM_152443.3 | P1 | |
RDH12 | ENST00000267502.3 | c.379G>T | p.Gly127Ter | stop_gained | 5/8 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Leber congenital amaurosis 13 Pathogenic:4
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2004 | - - |
Pathogenic, no assertion criteria provided | clinical testing | Payam Genetics Center, General Welfare Department of North Khorasan Province | Mar 01, 2023 | This variant has not been reported in the literature in individuals affected with RDH12-related conditions and Iranom. The 14 years old boy whit vision problem has been detected homozygous c.379G>T mutation on his RDH12 genes and the parents are first cousin. The RDH12 gene is associated whit autosomal recessive Leber congenital amaurosis 13/retinitis pigmentosa therefore he is affected to this disease. Therefore, it has been classified as a Variant of Pathogenic. - |
Pathogenic, no assertion criteria provided | research | Laboratory of Genetics in Ophthalmology, Institut Imagine | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Mar 05, 2019 | For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in RDH12 are known to be pathogenic (PMID: 17964524, 22065924). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has been observed in individuals affected with retinal dystrophies (PMID: 15322982, 17389517, 26355662). ClinVar contains an entry for this variant (Variation ID: 2051). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gly127*) in the RDH12 gene. It is expected to result in an absent or disrupted protein product. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2019 | - - |
Retinitis pigmentosa Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet | Apr 01, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
A;A;A
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at