rs5747933

Positions:

• chr22-18922842-G-A
• chr22-18922842-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The ENST00000357068.11(PRODH):​c.824C>T​(p.Thr275Ile) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T275N) has been classified as Benign.

• Frequency: Genomes: not found (cov: 0)
• Consequence: PRODH ENST00000357068.11 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08710632).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRODH	NM_016335.6	c.824C>T	p.Thr275Ile	missense_variant	6/14	ENST00000357068.11	NP_057419.5
PRODH	NM_001195226.2	c.500C>T	p.Thr167Ile	missense_variant	6/14		NP_001182155.2
PRODH	NM_001368250.2	c.500C>T	p.Thr167Ile	missense_variant	6/14		NP_001355179.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRODH	ENST00000357068.11	c.824C>T	p.Thr275Ile	missense_variant	6/14	1	NM_016335.6	ENSP00000349577	P3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.0000159 AC: 4 AN: 251154 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135812

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000352

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ExAC AF: 0.0000247 AC: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	2.4
DANN	Uncertain	0.98
DEOGEN2	Benign	0.028	T;.;.;T;T
Eigen	Benign	-0.87
Eigen_PC	Benign	-0.83
FATHMM_MKL	Benign	0.050	N
LIST_S2	Benign	0.67	T;.;T;.;T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.087	T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	1.0	N;N;N
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-1.7	.;N;N;N;N
REVEL	Benign	0.034
Sift	Benign	0.39	.;T;T;T;T
Sift4G	Benign	0.47	T;T;T;T;T
Polyphen		0.0040	.;B;B;.;.
Vest4		0.17
MutPred		0.66		Gain of helix (P = 0.0425);.;.;Gain of helix (P = 0.0425);.;
MVP		0.030
MPC		0.31
ClinPred		0.054	T
GERP RS		0.76
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5747933; hg19: chr22-18910355;