4-10019000-A-C
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP3_ModeratePP5_Very_Strong
The NM_020041.3(SLC2A9):āc.224T>Gā(p.Leu75Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000335 in 1,550,236 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 Likely pathogenic (ā ā ).
Frequency
Consequence
NM_020041.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000647 AC: 1AN: 154650Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81758
GnomAD4 exome AF: 0.0000343 AC: 48AN: 1398072Hom.: 0 Cov.: 33 AF XY: 0.0000290 AC XY: 20AN XY: 689526
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
Hypouricemia, renal, 2 Pathogenic:2
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SLC2A9-related disorder Pathogenic:1
The SLC2A9 c.224T>G variant is predicted to result in the amino acid substitution p.Leu75Arg. This variant has been reported in an individuals with autosomal recessive renal hypouricaemia, and functional studies support its pathogenicity (Dinour et al 2010. PubMed ID: 19926891; Ruiz A et al 2018. PubMed ID: 29967582; Capalbo A et al 2019. PubMed ID: 31589614). This variant is reported in 0.0040% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/4-10020624-A-C). This variant is interpreted as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at