chrX-37686138-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_021083.4(XK):c.177C>G(p.His59Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000132 in 1,209,398 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. 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. H59R) has been classified as Uncertain significance.
Frequency
Consequence
NM_021083.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XK | NM_021083.4 | c.177C>G | p.His59Gln | missense_variant | 1/3 | ENST00000378616.5 | |
XK | XM_011543978.4 | c.177C>G | p.His59Gln | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XK | ENST00000378616.5 | c.177C>G | p.His59Gln | missense_variant | 1/3 | 1 | NM_021083.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000353 AC: 4AN: 113340Hom.: 0 Cov.: 24 AF XY: 0.0000282 AC XY: 1AN XY: 35472
GnomAD3 exomes AF: 0.0000114 AC: 2AN: 174742Hom.: 0 AF XY: 0.0000161 AC XY: 1AN XY: 62054
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1096058Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 361716
GnomAD4 genome ? AF: 0.0000353 AC: 4AN: 113340Hom.: 0 Cov.: 24 AF XY: 0.0000282 AC XY: 1AN XY: 35472
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.177C>G (p.H59Q) alteration is located in exon 1 (coding exon 1) of the XK gene. This alteration results from a C to G substitution at nucleotide position 177, causing the histidine (H) at amino acid position 59 to be replaced by a glutamine (Q). 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