6-65495231-CA-CAA
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001142800.2(EYS):c.179dupT(p.Leu60PhefsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001142800.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.179dupT | p.Leu60PhefsTer6 | frameshift_variant | Exon 4 of 43 | ENST00000503581.6 | NP_001136272.1 | |
EYS | NM_001292009.2 | c.179dupT | p.Leu60PhefsTer6 | frameshift_variant | Exon 4 of 44 | NP_001278938.1 | ||
EYS | NM_001142801.2 | c.179dupT | p.Leu60PhefsTer6 | frameshift_variant | Exon 4 of 12 | NP_001136273.1 | ||
EYS | NM_198283.2 | c.179dupT | p.Leu60PhefsTer6 | frameshift_variant | Exon 3 of 10 | NP_938024.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This variant has not been reported in the literature in individuals affected with EYS-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu60Phefs*6) in the EYS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EYS are known to be pathogenic (PMID: 18836446, 20333770). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.