chrX-154156469-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PS1_ModeratePM2PP3_Strong
The NM_020061.6(OPN1LW):c.920C>T(p.Pro307Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000733 in 1,091,952 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_020061.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN1LW | NM_020061.6 | c.920C>T | p.Pro307Leu | missense_variant | 5/6 | ENST00000369951.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN1LW | ENST00000369951.9 | c.920C>T | p.Pro307Leu | missense_variant | 5/6 | 1 | NM_020061.6 | P1 | |
OPN1LW | ENST00000442922.1 | c.384+125C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 19
GnomAD3 exomes AF: 0.00000549 AC: 1AN: 182181Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66791
GnomAD4 exome AF: 0.00000733 AC: 8AN: 1091952Hom.: 0 Cov.: 32 AF XY: 0.00000280 AC XY: 1AN XY: 357612
GnomAD4 genome ? Cov.: 19
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 07, 2022 | Variant observed in a patient with severe congenital color blindness in the literature (Nathans et al., 1993); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8213841) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at