19-35800150-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_021232.2(PRODH2):c.1271G>A(p.Arg424Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000623 in 1,605,122 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021232.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRODH2 | NM_021232.2 | c.1271G>A | p.Arg424Gln | missense_variant | Exon 10 of 10 | ENST00000653904.2 | NP_067055.2 | |
PRODH2 | NM_001378292.1 | c.1115G>A | p.Arg372Gln | missense_variant | Exon 9 of 9 | NP_001365221.1 | ||
PRODH2 | NM_001378293.1 | c.*48G>A | 3_prime_UTR_variant | Exon 9 of 9 | NP_001365222.1 | |||
PRODH2 | NM_001378294.1 | c.*48G>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.1271G>A | p.Arg424Gln | missense_variant | Exon 10 of 10 | NM_021232.2 | ENSP00000499779.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 28AN: 232582Hom.: 1 AF XY: 0.0000953 AC XY: 12AN XY: 125936
GnomAD4 exome AF: 0.0000564 AC: 82AN: 1452790Hom.: 2 Cov.: 31 AF XY: 0.0000582 AC XY: 42AN XY: 721922
GnomAD4 genome AF: 0.000118 AC: 18AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1499G>A (p.R500Q) 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 1499, causing the arginine (R) at amino acid position 500 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