17-42543882-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000263.4(NAGLU):āc.1876C>Gā(p.Arg626Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,604,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R626Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000263.4 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 |
---|---|---|---|---|---|---|---|
NAGLU | NM_000263.4 | c.1876C>G | p.Arg626Gly | missense_variant | 6/6 | ENST00000225927.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAGLU | ENST00000225927.7 | c.1876C>G | p.Arg626Gly | missense_variant | 6/6 | 1 | NM_000263.4 | P1 | |
NAGLU | ENST00000591587.1 | c.*845C>G | 3_prime_UTR_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000436 AC: 1AN: 229530Hom.: 0 AF XY: 0.00000800 AC XY: 1AN XY: 125032
GnomAD4 exome AF: 0.0000227 AC: 33AN: 1452088Hom.: 0 Cov.: 32 AF XY: 0.0000180 AC XY: 13AN XY: 721698
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at