rs773450573

chr17-47946682-G-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_018129.4(PNPO):c.686G>A(p.Arg229Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 11/18 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R229W) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000014 (0 hom.)
• Consequence: PNPO NM_018129.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11
• Conservation: PhyloP100: 9.64

Genes affected

PNPO (HGNC:30260): (pyridoxamine 5'-phosphate oxidase) The enzyme encoded by this gene catalyzes the terminal, rate-limiting step in the synthesis of pyridoxal 5'-phosphate, also known as vitamin B6. Vitamin B6 is a required co-factor for enzymes involved in both homocysteine metabolism and synthesis of neurotransmitters such as catecholamine. Mutations in this gene result in pyridoxamine 5'-phosphate oxidase (PNPO) deficiency, a form of neonatal epileptic encephalopathy. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a chain Pyridoxine-5'-phosphate oxidase (size 260) in uniprot entity PNPO_HUMAN there are 19 pathogenic changes around while only 2 benign (90%) in NM_018129.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-47946681-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 6523.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.993
• PP5: Variant 17-47946682-G-A is Pathogenic according to our data. Variant chr17-47946682-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 206452.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-47946682-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNPO	NM_018129.4	c.686G>A	p.Arg229Gln	missense_variant	7/7	ENST00000642017.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNPO	ENST00000642017.2	c.686G>A	p.Arg229Gln	missense_variant	7/7		NM_018129.4	P1

Frequencies

GnomAD3 genomes AF: 0.0000328 AC: 5 AN: 152230 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000119 AC: 3 AN: 251476 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135912

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000144 AC: 21 AN: 1461848 Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15 AN XY: 727222

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000135

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000328 AC: 5 AN: 152230 Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4 AN XY: 74366

Gnomad4 AFR AF: 0.0000724

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000971 Hom.: 0

Bravo AF: 0.0000227

ExAC AF: 0.0000165 AC: 2

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Pyridoxal phosphate-responsive seizures Pathogenic:8

Pathogenic, no assertion criteria provided	research	Gene Discovery Core-Manton Center, Boston Children's Hospital	Feb 14, 2020	This variant is interpretted as Pathogenic for Pyridoxamine 5'-phosphate oxidase deficiency, Austomal Recessive. PM1 - Located in a mutational hot spot and/or critical and well-established functional domain without benign variation. PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PM5 - Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before (PMID: 24645144). PP2 - Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease. PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation (PMID: 26077850). -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 19, 2023	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 229 of the PNPO protein (p.Arg229Gln). This variant is present in population databases (rs773450573, gnomAD 0.008%). This missense change has been observed in individual(s) with PNPO related disease (PMID: 23708187, 24266778, 28133863, 28985901). ClinVar contains an entry for this variant (Variation ID: 206452). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PNPO protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 31, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 25, 2023	Variant summary: PNPO c.686G>A (p.Arg229Gln) results in a conservative amino acid change in the encoded protein sequence. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251476 control chromosomes (gnomAD). c.686G>A has been reported in the literature in at least two homozygous individuals affected with Pyridoxal 5'-Phosphate-Dependent Epilepsy (e.g. Ware_2013, Carvill_2013, Guerriero_2017, Olson_2017, Kingsmore_2022). These data indicate that the variant is likely to be associated with disease. At least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated that the variant severely decreased enzymatic activity (both Km and Vmax) compared to the WT (Musayev_2009). The following publications have been ascertained in the context of this evaluation (PMID: 24266778, 23708187, 28985901, 28133863, 36007526, 19759001). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	research	Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre	Apr 29, 2021	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Feb 09, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 07, 2020	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Pathogenic, no assertion criteria provided	clinical testing	Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare	Sep 18, 2017	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 28, 2018	The R229Q variant in the PNPO gene has been reported previously in the homozygous state in two unrelated children with early epileptic encephalopathy and in another individual with an unspecified neurocognitive phenotype (Carvill et al., 2013; Ware et al., 2014; Yavarna et al., 2015). The R229Q variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R229Q variant is a semi-conservative amino acid substitution, which occurs at a position that is conserved across species and lies within a region of the protein necessary for substrate binding and catalysis (Musayev et al., 2009). In silico analysis predicts this variant is probably damaging to the protein structure/function. A different missense substitution at the same position (R229W) has also been published in association with PNPO deficiency (Mills et al., 2005), supporting the functional importance of this region of the protein. We interpret R229Q as a pathogenic variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Oct 28, 2019	This variant has been reported in the homozygous state in multiple families with PNPOD (PMID: 28985901, 24266778). Assessment of experimental evidence suggests this variant results in reduced catalytic efficiency (PMID: 19759001). The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org).This observation is not an independent occurrence and has been identified in the same individual by RCIGM, the other laboratory participating in the GEMINI study. -

PNPO-related condition Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 15, 2023

The PNPO c.686G>A variant is predicted to result in the amino acid substitution p.Arg229Gln. This variant has been reported in the homozygous state in multiple individuals with PNPO-related epilepsy (see for example, Carvill et al. 2013. PubMed ID: 23708187; Olson et al. 2017. PubMed ID: 28133863; Guerriero et al. 2017. PubMed ID: 28985901; Maron et al. 2021. PubMed ID: 33587123). This variant is reported in 0.0080% of alleles in individuals of African descent in gnomAD. A different missense variant affecting the same amino acid (p.Arg229Trp) has been associated with PNPO-related epilepsy in a family; however, the evidence was indirect (Mills et al. 2005. PubMed ID: 15772097). Taken together, the c.686G>A (p.Arg229Gln) variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.92
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.61
Cadd	Pathogenic	34
Dann	Pathogenic	1.0
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.92
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	1.0	D;D;D;D;D
M_CAP	Pathogenic	0.82	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.75	T
Polyphen		1.0	.;D;.;.;.
MutPred		0.97		.;Loss of MoRF binding (P = 0.0149);.;.;.;
MVP		0.99
MPC		1.5
ClinPred		1.0	D
GERP RS		5.2
Varity_R		0.99
gMVP		0.86

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: rs773450573; hg19: chr17-46024048;