rs104894933
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_000330.4(RS1):c.221G>T(p.Gly74Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000165 in 1,208,964 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. G74G) has been classified as Likely benign.
Frequency
Consequence
NM_000330.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.221G>T | p.Gly74Val | missense_variant | 4/6 | ENST00000379984.4 | |
RS1 | XM_047442337.1 | c.125G>T | p.Gly42Val | missense_variant | 2/4 | ||
CDKL5 | NM_001037343.2 | c.2797+1206C>A | intron_variant | ||||
CDKL5 | NM_003159.3 | c.2797+1206C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RS1 | ENST00000379984.4 | c.221G>T | p.Gly74Val | missense_variant | 4/6 | 1 | NM_000330.4 | P1 | |
CDKL5 | ENST00000379989.6 | c.2797+1206C>A | intron_variant | 1 | |||||
CDKL5 | ENST00000379996.7 | c.2797+1206C>A | intron_variant | 1 | |||||
RS1 | ENST00000476595.1 | n.712G>T | non_coding_transcript_exon_variant | 3/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000899 AC: 1AN: 111244Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33430
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097720Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 363148
GnomAD4 genome ? AF: 0.00000899 AC: 1AN: 111244Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33430
ClinVar
Submissions by phenotype
not provided Pathogenic:1Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
not provided, no classification provided | literature only | Retina International | - | - - |
Juvenile retinoschisis Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at