chrX-134473377-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000194.3(HPRT1):c.46G>A(p.Gly16Ser) 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,other (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G16V) 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 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPRT1 | NM_000194.3 | c.46G>A | p.Gly16Ser | missense_variant | 2/9 | ENST00000298556.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPRT1 | ENST00000298556.8 | c.46G>A | p.Gly16Ser | missense_variant | 2/9 | 1 | NM_000194.3 | P1 | |
HPRT1 | ENST00000462974.5 | n.204G>A | non_coding_transcript_exon_variant | 2/8 | 3 | ||||
HPRT1 | ENST00000475720.1 | n.4G>A | non_coding_transcript_exon_variant | 1/8 | 3 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 25
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 1991 | - - |
HPRT URANGAN Other:1
other, no assertion criteria provided | literature only | OMIM | May 12, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at