chr5-151281037-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_181774.4(SLC36A3):c.1121G>A(p.Arg374His) variant causes a missense change. The variant allele was found at a frequency of 0.0000297 in 1,614,070 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. R374C) has been classified as Uncertain significance.
Frequency
Consequence
NM_181774.4 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 |
---|---|---|---|---|---|---|---|
SLC36A3 | NM_181774.4 | c.1121G>A | p.Arg374His | missense_variant | 9/10 | ENST00000335230.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC36A3 | ENST00000335230.8 | c.1121G>A | p.Arg374His | missense_variant | 9/10 | 1 | NM_181774.4 | P1 | |
SLC36A3 | ENST00000377713.3 | c.1244G>A | p.Arg415His | missense_variant | 10/11 | 1 | |||
SLC36A3 | ENST00000423071.2 | n.3021G>A | non_coding_transcript_exon_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251136Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135696
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461844Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 727230
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.1244G>A (p.R415H) alteration is located in exon 10 (coding exon 10) of the SLC36A3 gene. This alteration results from a G to A substitution at nucleotide position 1244, causing the arginine (R) at amino acid position 415 to be replaced by a histidine (H). 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