rs1807467
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PS1_ModerateBP4_ModerateBP6BS2
The NM_016335.6(PRODH):c.1363G>T(p.Ala455Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_016335.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRODH | NM_016335.6 | c.1363G>T | p.Ala455Ser | missense_variant | 11/14 | ENST00000357068.11 | |
PRODH | NM_001195226.2 | c.1039G>T | p.Ala347Ser | missense_variant | 11/14 | ||
PRODH | NM_001368250.2 | c.1039G>T | p.Ala347Ser | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRODH | ENST00000357068.11 | c.1363G>T | p.Ala455Ser | missense_variant | 11/14 | 1 | NM_016335.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00116 AC: 24AN: 20746Hom.: 1 Cov.: 4
GnomAD3 exomes AF: 0.000941 AC: 236AN: 250766Hom.: 1 AF XY: 0.00105 AC XY: 143AN XY: 135618
GnomAD4 exome AF: 0.00184 AC: 397AN: 215336Hom.: 20 Cov.: 0 AF XY: 0.00175 AC XY: 199AN XY: 113760
GnomAD4 genome ? AF: 0.00115 AC: 24AN: 20796Hom.: 1 Cov.: 4 AF XY: 0.00107 AC XY: 10AN XY: 9358
ClinVar
Submissions by phenotype
Proline dehydrogenase deficiency Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 12, 2022 | This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 455 of the PRODH protein (p.Ala455Ser). This variant is present in population databases (rs1807467, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with PRODH-related conditions. ClinVar contains an entry for this variant (Variation ID: 4009). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Experimental studies have shown that this missense change affects PRODH function (PMID: 15662599). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2005 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 09, 2021 | The c.1363G>T (p.A455S) alteration is located in exon 12 (coding exon 11) of the PRODH gene. This alteration results from a G to T substitution at nucleotide position 1363, causing the alanine (A) at amino acid position 455 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | PRODH: BP4, BS2 - |
Schizophrenia 4 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Mar 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at