Variant rs1863134 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_012293.3(PXDN):c.2661C>T(p.Ser887Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00865 in 1,612,636 control chromosomes in the GnomAD database, including 905 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.044 ( 463 hom., cov: 32)

Exomes 𝑓: 0.0050 ( 442 hom. )

Consequence

PXDN
NM_012293.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0520

Variant links:

Genes affected

PXDN (HGNC:14966): (peroxidasin) This gene encodes a heme-containing peroxidase that is secreted into the extracellular matrix. It is involved in extracellular matrix formation, and may function in the physiological and pathological fibrogenic response in fibrotic kidney. Mutations in this gene cause corneal opacification and other ocular anomalies, and also microphthalmia and anterior segment dysgenesis. [provided by RefSeq, Aug 2014]

PXDN links:

PXDN (HGNC:):

PXDN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 2-1649119-G-A is Benign according to our data. Variant chr2-1649119-G-A is described in ClinVar as [Benign]. Clinvar id is 260222.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.052 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PXDN	NM_012293.3 linkuse as main transcript	c.2661C>T	p.Ser887Ser	synonymous_variant	17/23	ENST00000252804.9	NP_036425.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PXDN	ENST00000252804.9 linkuse as main transcript	c.2661C>T	p.Ser887Ser	synonymous_variant	17/23	1	NM_012293.3	ENSP00000252804.4		Q92626-1
PXDN	ENST00000478155.5 linkuse as main transcript	n.2697-4367C>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0439

AC:

6674

AN:

151986

Hom.:

462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0170

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00814

Gnomad SAS

AF:

0.00601

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000529

Gnomad OTH

AF:

0.0450

GnomAD3 exomes

AF:

0.0120

AC:

2947

AN:

245288

Hom.:

197

AF XY:

0.00968

AC XY:

1297

AN XY:

133972

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.00747

Gnomad ASJ exome

AF:

0.000503

Gnomad EAS exome

AF:

0.00598

Gnomad SAS exome

AF:

0.00462

Gnomad FIN exome

AF:

0.0000466

Gnomad NFE exome

AF:

0.000408

Gnomad OTH exome

AF:

0.00752

GnomAD4 exome

AF:

0.00496

AC:

7251

AN:

1460532

Hom.:

442

Cov.:

AF XY:

0.00444

AC XY:

3227

AN XY:

726552

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.00868

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.00237

Gnomad4 SAS exome

AF:

0.00424

Gnomad4 FIN exome

AF:

0.0000382

Gnomad4 NFE exome

AF:

0.000360

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.0440

AC:

6695

AN:

152104

Hom.:

463

Cov.:

AF XY:

0.0427

AC XY:

3176

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.150

Gnomad4 AMR

AF:

0.0169

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00816

Gnomad4 SAS

AF:

0.00602

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000529

Gnomad4 OTH

AF:

0.0450

Alfa

AF:

0.0201

Hom.:

Bravo

AF:

0.0497

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.000436

EpiControl

AF:

0.000711

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 31, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Anterior segment dysgenesis 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

8.6

DANN

Benign

0.80

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over