16-31484874-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003041.4(SLC5A2):c.254C>A(p.Ala85Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging 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 Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A2 | NM_003041.4 | c.254C>A | p.Ala85Glu | missense_variant | 3/14 | ENST00000330498.4 | |
SLC5A2 | XM_006721072.5 | c.254C>A | p.Ala85Glu | missense_variant | 3/13 | ||
SLC5A2 | XM_024450402.2 | c.254C>A | p.Ala85Glu | missense_variant | 3/11 | ||
SLC5A2 | NR_130783.2 | n.268C>A | non_coding_transcript_exon_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A2 | ENST00000330498.4 | c.254C>A | p.Ala85Glu | missense_variant | 3/14 | 1 | NM_003041.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251146Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135806
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461758Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727186
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.254C>A (p.A85E) alteration is located in exon 3 (coding exon 3) of the SLC5A2 gene. This alteration results from a C to A substitution at nucleotide position 254, causing the alanine (A) at amino acid position 85 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at