rs147530802

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000225873.9(PEX12):​c.102A>T​(p.Arg34Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00509 in 1,614,094 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R34K) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0050 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0051 ( 41 hom. )

Consequence

PEX12
ENST00000225873.9 missense

Scores

1
8
9

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:14

Conservation

PhyloP100: 1.26
Variant links:
Genes affected
PEX12 (HGNC:8854): (peroxisomal biogenesis factor 12) This gene belongs to the peroxin-12 family. Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are a group of genetically heterogeneous autosomal recessive, lethal diseases characterized by multiple defects in peroxisome function. The peroxisomal biogenesis disorders are a heterogeneous group with at least 14 complementation groups and with more than 1 phenotype being observed in cases falling into particular complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene are a cause of Zellweger syndrome (ZWS). [provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.012576401).
BP6
Variant 17-35577920-T-A is Benign according to our data. Variant chr17-35577920-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 92773.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-35577920-T-A is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00497 (757/152226) while in subpopulation NFE AF= 0.0062 (422/68012). AF 95% confidence interval is 0.00572. There are 5 homozygotes in gnomad4. There are 397 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PEX12NM_000286.3 linkuse as main transcriptc.102A>T p.Arg34Ser missense_variant 1/3 ENST00000225873.9 NP_000277.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PEX12ENST00000225873.9 linkuse as main transcriptc.102A>T p.Arg34Ser missense_variant 1/31 NM_000286.3 ENSP00000225873 P1
PEX12ENST00000586663.2 linkuse as main transcriptc.102A>T p.Arg34Ser missense_variant 1/31 ENSP00000466894
PEX12ENST00000585380.1 linkuse as main transcriptc.102A>T p.Arg34Ser missense_variant 2/34 ENSP00000466280

Frequencies

GnomAD3 genomes
AF:
0.00498
AC:
757
AN:
152110
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000773
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00393
Gnomad ASJ
AF:
0.0141
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00518
Gnomad FIN
AF:
0.0142
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00620
Gnomad OTH
AF:
0.00766
GnomAD3 exomes
AF:
0.00573
AC:
1442
AN:
251440
Hom.:
14
AF XY:
0.00611
AC XY:
830
AN XY:
135908
show subpopulations
Gnomad AFR exome
AF:
0.000369
Gnomad AMR exome
AF:
0.00301
Gnomad ASJ exome
AF:
0.0127
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00483
Gnomad FIN exome
AF:
0.0134
Gnomad NFE exome
AF:
0.00629
Gnomad OTH exome
AF:
0.00815
GnomAD4 exome
AF:
0.00511
AC:
7464
AN:
1461868
Hom.:
41
Cov.:
31
AF XY:
0.00525
AC XY:
3815
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.000627
Gnomad4 AMR exome
AF:
0.00362
Gnomad4 ASJ exome
AF:
0.0122
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00512
Gnomad4 FIN exome
AF:
0.0121
Gnomad4 NFE exome
AF:
0.00496
Gnomad4 OTH exome
AF:
0.00498
GnomAD4 genome
AF:
0.00497
AC:
757
AN:
152226
Hom.:
5
Cov.:
32
AF XY:
0.00533
AC XY:
397
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.000770
Gnomad4 AMR
AF:
0.00393
Gnomad4 ASJ
AF:
0.0141
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00539
Gnomad4 FIN
AF:
0.0142
Gnomad4 NFE
AF:
0.00620
Gnomad4 OTH
AF:
0.00758
Alfa
AF:
0.00602
Hom.:
3
Bravo
AF:
0.00365
TwinsUK
AF:
0.00431
AC:
16
ALSPAC
AF:
0.00649
AC:
25
ESP6500AA
AF:
0.000681
AC:
3
ESP6500EA
AF:
0.00709
AC:
61
ExAC
AF:
0.00574
AC:
697
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:14
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:5
Benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)May 02, 2014- -
Benign, no assertion criteria providedclinical testingGenome Diagnostics Laboratory, University Medical Center Utrecht-- -
Likely benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 28, 2016Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Benign by Emory 2014. Has been reported in 2 homozygous individuals of iranian origin, who presented with peroxisomal biogenesis disorder with mild clinical phenotype. Consanguinity in at least one of the families. (Zeharia 2007). Given the high frequency in ExAC, LB -
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJun 14, 2022Variant summary: PEX12 c.102A>T (p.Arg34Ser) results in a non-conservative amino acid change located in the Pex, N-terminal domain (IPR006845) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0058 in 282832 control chromosomes in the gnomAD database, including 17 homozygotes. The observed variant frequency is approximately 4 fold of the estimated maximal expected allele frequency for a pathogenic variant in PEX12 causing Zellweger Syndrome (0.0016), strongly suggesting that the variant is benign. Six ClinVar submitters have assessed the variant since 2014: two classified the variant as likely benign and four as benign. Based on the evidence outlined above, the variant was classified as benign. -
not provided Benign:4
Benign, criteria provided, single submitterclinical testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsSep 18, 2017- -
Benign, criteria provided, single submitterclinical testingGeneDxDec 09, 2020This variant is associated with the following publications: (PMID: 26643206, 17534573, 15542397) -
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJun 01, 2024PEX12: BS1, BS2 -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Peroxisome biogenesis disorder 3A (Zellweger) Benign:2
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaApr 27, 2017This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -
Peroxisome biogenesis disorder type 3B Benign:1
Benign, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -
Peroxisome biogenesis disorder type 3B;C3553929:Peroxisome biogenesis disorder 3A (Zellweger) Benign:1
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsApr 12, 2022- -
PEX12-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesFeb 14, 2020This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.10
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.29
T;T;T
Eigen
Benign
0.19
Eigen_PC
Benign
0.19
FATHMM_MKL
Uncertain
0.76
D
LIST_S2
Uncertain
0.92
.;D;D
MetaRNN
Benign
0.013
T;T;T
MetaSVM
Benign
-0.61
T
MutationAssessor
Benign
1.8
L;L;.
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.54
T
PROVEAN
Uncertain
-2.6
D;.;.
REVEL
Uncertain
0.54
Sift
Uncertain
0.012
D;.;.
Sift4G
Uncertain
0.015
D;D;D
Polyphen
0.92
P;P;.
Vest4
0.45
MutPred
0.93
Loss of methylation at R34 (P = 0.0939);Loss of methylation at R34 (P = 0.0939);Loss of methylation at R34 (P = 0.0939);
MVP
0.77
MPC
0.46
ClinPred
0.027
T
GERP RS
3.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.49
gMVP
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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

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

Other links and lift over

dbSNP: rs147530802; hg19: chr17-33904939; API