16-31484724-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_003041.4(SLC5A2):c.178C>T(p.Arg60Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000429 in 1,609,992 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 (★★).
Frequency
Consequence
NM_003041.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC5A2 | NM_003041.4 | c.178C>T | p.Arg60Cys | missense_variant | Exon 2 of 14 | ENST00000330498.4 | NP_003032.1 | |
SLC5A2 | XM_006721072.5 | c.178C>T | p.Arg60Cys | missense_variant | Exon 2 of 13 | XP_006721135.3 | ||
SLC5A2 | XM_024450402.2 | c.178C>T | p.Arg60Cys | missense_variant | Exon 2 of 11 | XP_024306170.2 | ||
SLC5A2 | NR_130783.2 | n.192C>T | non_coding_transcript_exon_variant | Exon 2 of 12 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248438Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134564
GnomAD4 exome AF: 0.0000446 AC: 65AN: 1457772Hom.: 0 Cov.: 32 AF XY: 0.0000386 AC XY: 28AN XY: 725390
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
SLC5A2-related disorder Uncertain:1
The SLC5A2 c.178C>T variant is predicted to result in the amino acid substitution p.Arg60Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0050% of alleles in individuals of East Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
not provided Uncertain:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Familial renal glucosuria Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at