chr8-42428829-C-T
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM2PP2PP3_StrongPP5_Very_Strong
The NM_001257180.2(SLC20A2):c.1723G>A(p.Glu575Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,448,922 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 Likely pathogenic (★★).
Frequency
Consequence
NM_001257180.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC20A2 | NM_001257180.2 | c.1723G>A | p.Glu575Lys | missense_variant | 10/11 | ENST00000520262.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC20A2 | ENST00000520262.6 | c.1723G>A | p.Glu575Lys | missense_variant | 10/11 | 2 | NM_001257180.2 | P1 | |
SLC20A2 | ENST00000342228.7 | c.1723G>A | p.Glu575Lys | missense_variant | 10/11 | 1 | P1 | ||
SLC20A2 | ENST00000520179.5 | c.1723G>A | p.Glu575Lys | missense_variant | 10/11 | 1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1448922Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 720416
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Idiopathic basal ganglia calcification 1 Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Jul 13, 2021 | PS3, PP2, PS4_Supporting, PM2 - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 12, 2012 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota | Nov 21, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at