NM_012293.3:c.831C>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_012293.3(PXDN):c.831C>A(p.Ile277Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
PXDN
NM_012293.3 synonymous
NM_012293.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.17
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- anterior segment dysgenesis 7Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, PanelApp Australia, ClinGen, Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 2-1676944-G-T is Benign according to our data. Variant chr2-1676944-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 471917.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.16 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012293.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PXDN | NM_012293.3 | MANE Select | c.831C>A | p.Ile277Ile | synonymous | Exon 8 of 23 | NP_036425.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PXDN | ENST00000252804.9 | TSL:1 MANE Select | c.831C>A | p.Ile277Ile | synonymous | Exon 8 of 23 | ENSP00000252804.4 | ||
| PXDN | ENST00000433670.5 | TSL:1 | c.816C>A | p.Ile272Ile | synonymous | Exon 8 of 16 | ENSP00000402738.1 | ||
| PXDN | ENST00000425171.2 | TSL:5 | c.759C>A | p.Ile253Ile | synonymous | Exon 7 of 16 | ENSP00000398363.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460096Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726054 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1460096
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
726054
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33470
American (AMR)
AF:
AC:
0
AN:
44584
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26088
East Asian (EAS)
AF:
AC:
0
AN:
39672
South Asian (SAS)
AF:
AC:
0
AN:
85550
European-Finnish (FIN)
AF:
AC:
0
AN:
53330
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111300
Other (OTH)
AF:
AC:
0
AN:
60336
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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10
<30
30-35
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Anterior segment dysgenesis 7 Benign:1
Sep 01, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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