rs561449819
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002340.6(LSS):c.1762G>C(p.Gly588Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,528 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G588S) has been classified as Uncertain significance.
Frequency
Consequence
NM_002340.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LSS | NM_002340.6 | c.1762G>C | p.Gly588Arg | missense_variant | 19/22 | ENST00000397728.8 | |
LSS | NM_001001438.3 | c.1762G>C | p.Gly588Arg | missense_variant | 19/23 | ||
LSS | NM_001145436.2 | c.1729G>C | p.Gly577Arg | missense_variant | 19/22 | ||
LSS | NM_001145437.2 | c.1522G>C | p.Gly508Arg | missense_variant | 18/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LSS | ENST00000397728.8 | c.1762G>C | p.Gly588Arg | missense_variant | 19/22 | 1 | NM_002340.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250896Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135626
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461528Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727002
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at