19-35800132-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021232.2(PRODH2):c.1289G>A(p.Arg430Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,455,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign 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. R430L) has been classified as Uncertain significance.
Frequency
Consequence
NM_021232.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRODH2 | NM_021232.2 | c.1289G>A | p.Arg430Gln | missense_variant | Exon 10 of 10 | ENST00000653904.2 | NP_067055.2 | |
PRODH2 | NM_001378292.1 | c.1133G>A | p.Arg378Gln | missense_variant | Exon 9 of 9 | NP_001365221.1 | ||
PRODH2 | NM_001378293.1 | c.*66G>A | 3_prime_UTR_variant | Exon 9 of 9 | NP_001365222.1 | |||
PRODH2 | NM_001378294.1 | c.*66G>A | 3_prime_UTR_variant | Exon 8 of 8 | NP_001365223.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRODH2 | ENST00000653904.2 | c.1289G>A | p.Arg430Gln | missense_variant | Exon 10 of 10 | NM_021232.2 | ENSP00000499779.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 237794Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128840
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1455860Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 723666
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1517G>A (p.R506Q) alteration is located in exon 11 (coding exon 11) of the PRODH2 gene. This alteration results from a G to A substitution at nucleotide position 1517, causing the arginine (R) at amino acid position 506 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