rs137852934
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PS1_ModerateBP4_StrongBP6
The NM_016335.6(PRODH):c.865T>A(p.Leu289Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/18 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRODH | NM_016335.6 | c.865T>A | p.Leu289Met | missense_variant | 7/14 | ENST00000357068.11 | |
PRODH | NM_001195226.2 | c.541T>A | p.Leu181Met | missense_variant | 7/14 | ||
PRODH | NM_001368250.2 | c.541T>A | p.Leu181Met | missense_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRODH | ENST00000357068.11 | c.865T>A | p.Leu289Met | missense_variant | 7/14 | 1 | NM_016335.6 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 exomes AF: 0.00361 AC: 904AN: 250616Hom.: 5 AF XY: 0.00369 AC XY: 500AN XY: 135494
GnomAD4 exome Cov.: 0
GnomAD4 genome ? Cov.: 0
ClinVar
Submissions by phenotype
Proline dehydrogenase deficiency Pathogenic:1Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Aug 07, 2018 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2005 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Schizophrenia 4 Uncertain:1Other:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Aug 07, 2018 | - - |
risk factor, no assertion criteria provided | literature only | OMIM | Mar 01, 2005 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Jul 27, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 18506409, 28202261, 12217952, 15662599, 24498354, 15494707) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at