chr5-1212338-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 8P and 2B. PP5_Very_StrongBP4BS1_Supporting
The NM_001003841.3(SLC6A19):c.517G>A(p.Asp173Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0031 in 1,613,638 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001003841.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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SLC6A19 | ENST00000304460.11 | c.517G>A | p.Asp173Asn | missense_variant | Exon 4 of 12 | 1 | NM_001003841.3 | ENSP00000305302.10 | ||
SLC6A19 | ENST00000515652.5 | n.425G>A | non_coding_transcript_exon_variant | Exon 4 of 11 | 2 | ENSP00000425701.1 |
Frequencies
GnomAD3 genomes AF: 0.00165 AC: 251AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00156 AC: 392AN: 250978Hom.: 0 AF XY: 0.00148 AC XY: 201AN XY: 135722
GnomAD4 exome AF: 0.00326 AC: 4758AN: 1461388Hom.: 12 Cov.: 33 AF XY: 0.00317 AC XY: 2303AN XY: 727024
GnomAD4 genome AF: 0.00164 AC: 250AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.00141 AC XY: 105AN XY: 74434
ClinVar
Submissions by phenotype
not provided Pathogenic:9
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Published functional studies have shown the SLC6A19 transport activity was reduced in the D173N construct compared to wild type (PMID: 19185582, 15286788); This variant is associated with the following publications: (PMID: 28787443, 15286788, 17555458, 25082825, 29431110, 30665703, 30487145, 31908951, 31980526, 34041853, 33848968, 31589614, 34426522, 18484095, 34297361, 19185582) -
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This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 173 of the SLC6A19 protein (p.Asp173Asn). This variant is present in population databases (rs121434346, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with Hartnup disorder (PMID: 15286788, 17555458, 18484095, 21814048). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2019). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SLC6A19 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects SLC6A19 function (PMID: 15286788, 19185582). For these reasons, this variant has been classified as Pathogenic. -
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PP1_moderate, PM3_very_strong, PS3_supporting -
Neutral 1 amino acid transport defect Pathogenic:6
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Variant summary: SLC6A19 c.517G>A (p.Asp173Asn) results in a conservative amino acid change to a highly conserved residue (HGMD) in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0016 in 250978 control chromosomes, predominantly at a frequency of 0.0031 within the Non-Finnish European subpopulation in the gnomAD database. c.517G>A has been reported in the literature in multiple individuals affected with Hartnup Disease (Seow_2004, Schuermans_2022), including those that were compound heterozygous with other pathogenic variants. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, finding that the variant resulted in <50% of wild type leucine transport activity (Seow_2004). The following publications have been ascertained in the context of this evaluation (PMID: 15286788, 35606766). 13 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as pathogenic (n=10), likely pathogenic (n=2), or uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -
The p.Asp173Asn (NM_001003841.2 c.517G>A) variant in the SLC6A19 gene has been r eported at least 10 individuals with Hartnup disease, 2 of whom were homozygous and 8 of whom were compound heterozygous with another SLC6A19 variant (Seow 2004 , Azmanov 2008). This is the most frequent pathogenic variant in patients of Eur opean descent (Azmanov 2007). This variant has also been reported in ClinVar (V ariation ID#2019), as pathogenic or likely pathogenic by three laboratories. In vitro studies indicate this variant causes a partial inactivation of the protein (Seow 2004, Camargo 2009). The p.Asp173Asn variant has been identified in 0.3% (384/126,562) of European chromosomes by the Genome Aggregation Database (gnomAD ; http://gnomad.broadinstitute.org; dbSNP rs121434346), though this frequency is low enough to be consistent with a recessive carrier frequency. In summary, th is variant meets our criteria to be classified as pathogenic for Hartnup disease in an autosomal recessive manner based on functional studies and its occurrence in individuals with this disease. -
SLC6A19-related disorder Pathogenic:1
The SLC6A19 c.517G>A variant is predicted to result in the amino acid substitution p.Asp173Asn. This variant has been reported in individuals with autosomal recessive Hartnup disorder and results in reduced transport activity compared to wild type (Seow et al. 2004. PubMed ID: 15286788; Camargo et al. 2009. PubMed ID: 19185582). This variant is reported in 0.30% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -
Neutral 1 amino acid transport defect;C0268654:Iminoglycinuria;C0543541:Hyperglycinuria Pathogenic:1
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not specified Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at