rs558960349
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001379110.1(SLC9A6):āc.1873A>Gā(p.Ser625Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,209,642 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001379110.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.1873A>G | p.Ser625Gly | missense_variant | 18/18 | ENST00000630721.3 | NP_001366039.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.1873A>G | p.Ser625Gly | missense_variant | 18/18 | 4 | NM_001379110.1 | ENSP00000487486 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111726Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33890
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183365Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67831
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097862Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 1AN XY: 363222
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111780Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33954
ClinVar
Submissions by phenotype
Christianson syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 10, 2023 | This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 615 of the SLC9A6 protein (p.Ser615Gly). This variant is present in population databases (rs558960349, gnomAD 0.008%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with SLC9A6-related conditions. ClinVar contains an entry for this variant (Variation ID: 537363). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at