chr14-67729200-T-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_152443.3(RDH12):c.668T>A(p.Val223Asp) 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V223F) has been classified as Likely pathogenic.
Frequency
Consequence
NM_152443.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDH12 | NM_152443.3 | c.668T>A | p.Val223Asp | missense_variant | 8/9 | ENST00000551171.6 | |
RDH12 | XM_047430965.1 | c.668T>A | p.Val223Asp | missense_variant | 8/9 | ||
ZFYVE26 | XM_047431173.1 | c.*542A>T | 3_prime_UTR_variant | 42/42 | |||
GPHN | XM_047430879.1 | c.1313-5995T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.668T>A | p.Val223Asp | missense_variant | 8/9 | 1 | NM_152443.3 | P1 | |
RDH12 | ENST00000267502.3 | c.668T>A | p.Val223Asp | missense_variant | 7/8 | 5 | P1 | ||
RDH12 | ENST00000552873.1 | n.37T>A | non_coding_transcript_exon_variant | 2/2 | 5 | ||||
ZFYVE26 | ENST00000394455.6 | n.3288+11A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Retinal dystrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at