4-25664267-G-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PS1PM2PP3_Strong
The NM_006424.3(SLC34A2):c.316G>A(p.Gly106Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000157 in 1,461,618 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 nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar.
Frequency
Consequence
NM_006424.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC34A2 | NM_006424.3 | c.316G>A | p.Gly106Arg | missense_variant | 4/13 | ENST00000382051.8 | |
SLC34A2 | NM_001177998.2 | c.313G>A | p.Gly105Arg | missense_variant | 4/13 | ||
SLC34A2 | NM_001177999.2 | c.313G>A | p.Gly105Arg | missense_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC34A2 | ENST00000382051.8 | c.316G>A | p.Gly106Arg | missense_variant | 4/13 | 1 | NM_006424.3 | P4 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251480Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135912
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461618Hom.: 0 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 727150
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at