rs146571352
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_033109.5(PNPT1):c.1525G>A(p.Val509Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00195 in 1,608,332 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 12 hom. )
Consequence
PNPT1
NM_033109.5 missense
NM_033109.5 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 7.36
Genes affected
PNPT1 (HGNC:23166): (polyribonucleotide nucleotidyltransferase 1) The protein encoded by this gene belongs to the evolutionary conserved polynucleotide phosphorylase family comprised of phosphate dependent 3'-to-5' exoribonucleases implicated in RNA processing and degradation. This enzyme is predominantly localized in the mitochondrial intermembrane space and is involved in import of RNA to mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency-13 and autosomal recessive nonsyndromic deafness-70. Related pseudogenes are found on chromosomes 3 and 7. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM1
?
In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_033109.5
BP4
?
Computational evidence support a benign effect (MetaRNN=0.16386932).
BS2
?
High Homozygotes in GnomAdExome4 at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPT1 | NM_033109.5 | c.1525G>A | p.Val509Ile | missense_variant | 19/28 | ENST00000447944.7 | |
PNPT1 | XM_005264629.3 | c.1285G>A | p.Val429Ile | missense_variant | 19/28 | ||
PNPT1 | XM_017005172.2 | c.1285G>A | p.Val429Ile | missense_variant | 18/27 | ||
PNPT1 | XM_047446161.1 | c.*57G>A | 3_prime_UTR_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPT1 | ENST00000447944.7 | c.1525G>A | p.Val509Ile | missense_variant | 19/28 | 1 | NM_033109.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00109 AC: 166AN: 152016Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000972 AC: 244AN: 250944Hom.: 1 AF XY: 0.000966 AC XY: 131AN XY: 135658
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GnomAD4 exome AF: 0.00204 AC: 2974AN: 1456200Hom.: 12 Cov.: 30 AF XY: 0.00197 AC XY: 1430AN XY: 724414
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GnomAD4 genome ? AF: 0.00109 AC: 166AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.000982 AC XY: 73AN XY: 74350
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:5Benign:3Other:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 27, 2023 | Variant summary: PNPT1 c.1525G>A (p.Val509Ile) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.002 in 1608332 control chromosomes in the gnomAD database, including 12 homozygotes, strongly suggesting the variant is a benign polymorphism. c.1525G>A has been reported in the literature in an individual affected with mild and chronic encephalopathy and deafness (Pennisi_2022). However, this report does not provide unequivocal conclusions about association of the variant with PNPT1-Related Disorders. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 33199448). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Four submitters classified the variant as uncertain significance and two classified it as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Oct 16, 2015 | - - |
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | PNPT1: BP4 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 24, 2023 | Observed in a patient with mitochondrial encephalopathy in published literature (Pennisi et al., 2020); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 26633545, 33199448, 34498404) - |
Combined oxidative phosphorylation defect type 13 Pathogenic:1
Likely pathogenic, flagged submission | clinical testing | Baylor Genetics | Feb 05, 2014 | Likely pathogenicity based on finding it once in our laboratory in trans with another variant [T531R] in an 18-year-old male with profound intellectual disability, severe bilateral hearing loss, hypotonia, dysmorphisms, short stature, microcephaly, hyperextensibility, myopia, cataract, congenital heart disease, fused kidneys, small testicles, type II diabetes, immunodeficiency (healthy sib NOT compound heterozygous). Variant likely pathogenic in recessive state; heterozygotes would be carriers. - |
Spinocerebellar ataxia type 25 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2021 | The c.1525G>A (p.V509I) alteration is located in exon 19 (coding exon 19) of the PNPT1 gene. This alteration results from a G to A substitution at nucleotide position 1525, causing the valine (V) at amino acid position 509 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Autosomal recessive nonsyndromic hearing loss 70;C4706283:Combined oxidative phosphorylation defect type 13 Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpretted as Uncertain significance and reported on 10/30/2014 by GTR ID 320384. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at