chrX-134473378-G-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_000194.3(HPRT1):c.47G>T(p.Gly16Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G16S) has been classified as Pathogenic.
Frequency
Consequence
NM_000194.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPRT1 | NM_000194.3 | c.47G>T | p.Gly16Val | missense_variant | 2/9 | ENST00000298556.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPRT1 | ENST00000298556.8 | c.47G>T | p.Gly16Val | missense_variant | 2/9 | 1 | NM_000194.3 | P1 | |
HPRT1 | ENST00000462974.5 | n.205G>T | non_coding_transcript_exon_variant | 2/8 | 3 | ||||
HPRT1 | ENST00000475720.1 | n.5G>T | non_coding_transcript_exon_variant | 1/8 | 3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 25
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Lesch-Nyhan syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris | Jan 06, 2017 | Intellectual disability, severe; tetradystonia; axial hypotonia; small degree of elevated uricemia - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at