rs949036081

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4

The NM_016335.6(PRODH):​c.130_156delACGGCAGTGCGGCCGCCGGTGCCCGCC​(p.Thr44_Ala52del) variant causes a conservative 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
NM_016335.6 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 1.99
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM4
Nonframeshift variant in NON repetitive region in NM_016335.6.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRODHNM_016335.6 linkuse as main transcriptc.130_156delACGGCAGTGCGGCCGCCGGTGCCCGCC p.Thr44_Ala52del conservative_inframe_deletion 1/14 ENST00000357068.11 NP_057419.5 O43272
PRODHNM_001195226.2 linkuse as main transcriptc.-52+232_-52+258delACGGCAGTGCGGCCGCCGGTGCCCGCC intron_variant NP_001182155.2 O43272
PRODHNM_001368250.2 linkuse as main transcriptc.-52+12_-52+38delACGGCAGTGCGGCCGCCGGTGCCCGCC intron_variant NP_001355179.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRODHENST00000357068.11 linkuse as main transcriptc.130_156delACGGCAGTGCGGCCGCCGGTGCCCGCC p.Thr44_Ala52del conservative_inframe_deletion 1/141 NM_016335.6 ENSP00000349577.6 O43272
ENSG00000283809ENST00000638240.1 linkuse as main transcriptc.514-3538_514-3512delGGGCACCGGCGGCCGCACTGCCGTGGC intron_variant 5 ENSP00000492446.1 A0A1W2PRQ8

Frequencies

GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.000224
Hom.:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Proline dehydrogenase deficiency;C1833247:Schizophrenia 4 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsAug 30, 2021- -
Proline dehydrogenase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicDec 28, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs949036081; hg19: chr22-18923644; API