rs121912697
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM5PP3_Moderate
The NM_000341.4(SLC3A1):c.1085G>A(p.Arg362His) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,614,132 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R362C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000341.4 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 |
---|---|---|---|---|---|---|---|
SLC3A1 | NM_000341.4 | c.1085G>A | p.Arg362His | missense_variant | 6/10 | ENST00000260649.11 | |
SLC3A1 | XM_011533047.4 | c.1085G>A | p.Arg362His | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A1 | ENST00000260649.11 | c.1085G>A | p.Arg362His | missense_variant | 6/10 | 1 | NM_000341.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251356Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135850
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727234
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74448
ClinVar
Submissions by phenotype
Cystinuria Pathogenic:1Uncertain:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2003 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 07, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at