rs74315353
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_007262.5(PARK7):āc.192G>Cā(p.Glu64Asp) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,528 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_007262.5 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.192G>C | p.Glu64Asp | missense_variant, splice_region_variant | 3/7 | ENST00000338639.10 | |
PARK7 | NM_001123377.2 | c.192G>C | p.Glu64Asp | missense_variant, splice_region_variant | 3/7 | ||
PARK7 | XM_005263424.4 | c.192G>C | p.Glu64Asp | missense_variant, splice_region_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.192G>C | p.Glu64Asp | missense_variant, splice_region_variant | 3/7 | 1 | NM_007262.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461358Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727034
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
Autosomal recessive early-onset Parkinson disease 7 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2004 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at