Genetic Variant NM_000318.3:c.748T>C (chr8-76983431-A-G) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM1BP4_StrongBP6BS1BS2

The NM_000318.3(PEX2):c.748T>C(p.Trp250Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00941 in 1,614,098 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W250G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0057 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0098 ( 104 hom. )

Consequence

PEX2
NM_000318.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:13

Conservation

PhyloP100: 8.73

Publications

8 publications found

Variant links:

Genes affected

PEX2 (HGNC:9717): (peroxisomal biogenesis factor 2) This gene encodes an integral peroxisomal membrane protein required for peroxisome biogenesis. The protein is thought to be involved in peroxisomal matrix protein import. Mutations in this gene result in one form of Zellweger syndrome and infantile Refsum disease. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

PEX2 Gene-Disease associations (from GenCC):

peroxisome biogenesis disorder
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
peroxisome biogenesis disorder 5A (Zellweger)
Inheritance: AR Classification: DEFINITIVE Submitted by: G2P, Myriad Women’s Health
peroxisome biogenesis disorder 5B
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
Zellweger spectrum disorders
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

PEX2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

PM1

In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 12 uncertain in NM_000318.3

BP4

Computational evidence support a benign effect (MetaRNN=0.015028745).

BP6

Variant 8-76983431-A-G is Benign according to our data. Variant chr8-76983431-A-G is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 129885.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00566 (861/152244) while in subpopulation NFE AF = 0.0101 (690/68008). AF 95% confidence interval is 0.00952. There are 3 homozygotes in GnomAd4. There are 372 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000318.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PEX2	NM_000318.3	MANE Select	c.748T>C	p.Trp250Arg	missense	Exon 4 of 4	NP_000309.2	P28328
PEX2	NM_001079867.2		c.748T>C	p.Trp250Arg	missense	Exon 3 of 3	NP_001073336.2	P28328
PEX2	NM_001172086.2		c.748T>C	p.Trp250Arg	missense	Exon 5 of 5	NP_001165557.2	P28328

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PEX2	ENST00000357039.9	TSL:1 MANE Select	c.748T>C	p.Trp250Arg	missense	Exon 4 of 4	ENSP00000349543.4	P28328
PEX2	ENST00000522527.5	TSL:1	c.748T>C	p.Trp250Arg	missense	Exon 3 of 3	ENSP00000428638.1	P28328
PEX2	ENST00000520103.5	TSL:2	c.748T>C	p.Trp250Arg	missense	Exon 3 of 3	ENSP00000428590.1	P28328

Frequencies

GnomAD3 genomes

AF:

0.00566

AC:

861

AN:

152126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00186

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00210

Gnomad ASJ

AF:

0.00691

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00245

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0101

Gnomad OTH

AF:

0.00287

GnomAD2 exomes

AF:

0.00526

AC:

1321

AN:

251326

AF XY:

0.00526

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.00377

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00277

Gnomad NFE exome

AF:

0.00935

Gnomad OTH exome

AF:

0.00554

GnomAD4 exome

AF:

0.00980

AC:

14320

AN:

1461854

Hom.:

104

Cov.:

AF XY:

0.00950

AC XY:

6910

AN XY:

727230

show subpopulations

African (AFR)

AF:

0.00149

AC:

AN:

33480

American (AMR)

AF:

0.00179

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00478

AC:

125

AN:

26136

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39698

South Asian (SAS)

AF:

0.00198

AC:

171

AN:

86258

European-Finnish (FIN)

AF:

0.00245

AC:

131

AN:

53394

Middle Eastern (MID)

AF:

0.00173

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0119

AC:

13204

AN:

1112000

Other (OTH)

AF:

0.00906

AC:

547

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

785

1570

2355

3140

3925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

500

1000

1500

2000

2500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00566

AC:

861

AN:

152244

Hom.:

Cov.:

AF XY:

0.00500

AC XY:

372

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.00185

AC:

AN:

41560

American (AMR)

AF:

0.00209

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00691

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5172

South Asian (SAS)

AF:

0.00124

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00245

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0101

AC:

690

AN:

68008

Other (OTH)

AF:

0.00284

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

130

174

217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00822

Hom.:

Bravo

AF:

0.00596

TwinsUK

AF:

0.0105

AC:

ALSPAC

AF:

0.0150

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.0119

AC:

102

ExAC

AF:

0.00499

AC:

606

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.0105

EpiControl

AF:

0.0101

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (5)

Peroxisome biogenesis disorder 5A (Zellweger) (4)

not specified (2)

Peroxisome biogenesis disorder 1A (Zellweger) (1)

Peroxisome biogenesis disorder 5B (1)

Zellweger spectrum disorders (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.80

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.10

CADD

Pathogenic

(source)

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.49

Eigen

Uncertain

0.56

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.51

MetaRNN

Benign

0.015

MetaSVM

Uncertain

-0.055

MutationAssessor

Benign

1.4

PhyloP100

8.7

PrimateAI

Uncertain

0.78

PROVEAN

Uncertain

-2.6

REVEL

Uncertain

0.55

Sift

Benign

0.72

Sift4G

Benign

0.77

Polyphen

1.0

Vest4

0.82

MutPred

0.68

Gain of disorder (P = 0.0331)

MVP

0.90

ClinPred

0.036

GERP RS

5.2

Varity_R

0.59

gMVP

0.73

Mutation Taster

=97/3

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over