rs748701094
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP3BS1_SupportingBS2
The NM_016335.6(PRODH):c.1765C>T(p.Arg589Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_016335.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRODH | NM_016335.6 | c.1765C>T | p.Arg589Trp | missense_variant | Exon 14 of 14 | ENST00000357068.11 | NP_057419.5 | |
PRODH | NM_001195226.2 | c.1441C>T | p.Arg481Trp | missense_variant | Exon 14 of 14 | NP_001182155.2 | ||
PRODH | NM_001368250.2 | c.1441C>T | p.Arg481Trp | missense_variant | Exon 14 of 14 | NP_001355179.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRODH | ENST00000357068.11 | c.1765C>T | p.Arg589Trp | missense_variant | Exon 14 of 14 | 1 | NM_016335.6 | ENSP00000349577.6 | ||
ENSG00000283809 | ENST00000638240.1 | c.513+2185G>A | intron_variant | Intron 4 of 5 | 5 | ENSP00000492446.1 |
Frequencies
GnomAD3 genomes AF: 0.000136 AC: 4AN: 29518Hom.: 2 Cov.: 0
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000122 AC: 6AN: 490868Hom.: 3 Cov.: 0 AF XY: 0.0000166 AC XY: 4AN XY: 241216
GnomAD4 genome AF: 0.000135 AC: 4AN: 29592Hom.: 2 Cov.: 0 AF XY: 0.000139 AC XY: 2AN XY: 14350
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1765C>T (p.R589W) alteration is located in exon 15 (coding exon 14) of the PRODH gene. This alteration results from a C to T substitution at nucleotide position 1765, causing the arginine (R) at amino acid position 589 to be replaced by a tryptophan (W). The p.R589W alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Proline dehydrogenase deficiency;C1833247:Schizophrenia 4 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at