rs104894278
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_000317.3(PTS):c.139A>G(p.Asn47Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,650 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). Synonymous variant affecting the same amino acid position (i.e. N47N) has been classified as Likely benign.
Frequency
Consequence
NM_000317.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTS | NM_000317.3 | c.139A>G | p.Asn47Asp | missense_variant | 2/6 | ENST00000280362.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTS | ENST00000280362.8 | c.139A>G | p.Asn47Asp | missense_variant | 2/6 | 1 | NM_000317.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250252Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135422
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460650Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 726668
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hyperphenylalaninemia, bh4-deficient, a, due to partial pts deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at