rs766076524
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_004174.4(SLC9A3):c.1145G>A(p.Arg382Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000842 in 1,544,770 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R382W) has been classified as Uncertain significance.
Frequency
Consequence
NM_004174.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.1145G>A | p.Arg382Gln | missense_variant | 6/17 | ENST00000264938.8 | |
SLC9A3 | NM_001284351.3 | c.1145G>A | p.Arg382Gln | missense_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.1145G>A | p.Arg382Gln | missense_variant | 6/17 | 1 | NM_004174.4 | P2 | |
SLC9A3 | ENST00000514375.1 | c.1145G>A | p.Arg382Gln | missense_variant | 6/17 | 1 | |||
SLC9A3 | ENST00000644203.1 | c.1145G>A | p.Arg382Gln | missense_variant | 6/16 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000125 AC: 2AN: 160016Hom.: 0 AF XY: 0.0000235 AC XY: 2AN XY: 85256
GnomAD4 exome AF: 0.00000862 AC: 12AN: 1392584Hom.: 0 Cov.: 32 AF XY: 0.0000102 AC XY: 7AN XY: 684938
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
Congenital secretory sodium diarrhea 8 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 06, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at