rs949036081
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The ENST00000357068.11(PRODH):c.130_156del(p.Thr44_Ala52del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: not found (cov: 0)
Consequence
PRODH
ENST00000357068.11 inframe_deletion
ENST00000357068.11 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.99
Genes affected
PRODH (HGNC:9453): (proline dehydrogenase 1) This gene encodes a mitochondrial protein that catalyzes the first step in proline degradation. Mutations in this gene are associated with hyperprolinemia type 1 and susceptibility to schizophrenia 4 (SCZD4). This gene is located on chromosome 22q11.21, a region which has also been associated with the contiguous gene deletion syndromes, DiGeorge and CATCH22. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in ENST00000357068.11.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRODH | NM_016335.6 | c.130_156del | p.Thr44_Ala52del | inframe_deletion | 1/14 | ENST00000357068.11 | NP_057419.5 | |
PRODH | NM_001195226.2 | c.-52+232_-52+258del | intron_variant | NP_001182155.2 | ||||
PRODH | NM_001368250.2 | c.-52+12_-52+38del | intron_variant | NP_001355179.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRODH | ENST00000357068.11 | c.130_156del | p.Thr44_Ala52del | inframe_deletion | 1/14 | 1 | NM_016335.6 | ENSP00000349577 | P3 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 0
GnomAD4 genome
Cov.:
0
Alfa
AF:
Hom.:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Proline dehydrogenase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 28, 2016 | - - |
Proline dehydrogenase deficiency;C1833247:Schizophrenia 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 30, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at