PXDN

peroxidasin, the group of I-set domain containing

Basic information

Region (hg38): 2:1631887-1744852

Links

ENSG00000130508 ∙ NCBI:7837 ∙ OMIM:605158 ∙ HGNC:14966 ∙ Uniprot:Q92626 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• anterior segment dysgenesis 7 (Strong), mode of inheritance: AR
• anterior segment dysgenesis 7 (Moderate), mode of inheritance: AR
• anterior segment dysgenesis 7 (Strong), mode of inheritance: AR
• anterior segment dysgenesis 7 (Supportive), mode of inheritance: AR
• anterior segment dysgenesis 7 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Anterior segment dysgenesis 7	AR	Ophthalmologic	Some individual are at risk of glaucoma, and surveillance and early treatment may be beneficial; Agents that may contribute to glaucoma should be avoided	Ophthalmologic	21907015; 24939590

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PXDN gene.

• Anterior segment dysgenesis 7 (11 variants)
• Anterior segment dysgenesis (1 variants)
• Glaucoma 3A (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXDN gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	84	23	108
missense	1		126	13	4	144
nonsense	5	1				6
start loss	1					1
frameshift	4					4
inframe indel			1			1
splice donor/acceptor (+/-2bp)	2	2				4
splice region			1	7	5	13
non coding				67	57	124
Total	13	3	128	164	84

Highest pathogenic variant AF is 0.0000132

Variants in PXDN

This is a list of pathogenic ClinVar variants found in the PXDN region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-1633876-T-C			Benign (Jun 26, 2018)
2-1634046-G-A			Likely benign (Sep 22, 2018)
2-1634203-C-A		not specified	Likely benign (-)
2-1634207-G-A		Anterior segment dysgenesis 7 • PXDN-related disorder	Benign/Likely benign (Dec 13, 2021)
2-1634219-C-T		Anterior segment dysgenesis 7	Likely benign (Aug 17, 2023)
2-1634257-G-A		Inborn genetic diseases	Uncertain significance (May 17, 2023)
2-1634266-C-T		Inborn genetic diseases	Likely benign (Mar 19, 2024)
2-1634287-G-T		Anterior segment dysgenesis 7	Uncertain significance (Oct 13, 2023)
2-1634302-C-T		Anterior segment dysgenesis 7	Uncertain significance (Jun 27, 2017)
2-1634303-G-A		Anterior segment dysgenesis 7	Benign (Dec 26, 2023)
2-1634339-G-A		Anterior segment dysgenesis 7	Benign/Likely benign (Jan 20, 2024)
2-1634446-G-C			Benign (Dec 12, 2018)
2-1634520-T-C			Likely benign (Sep 22, 2018)
2-1634563-G-A			Likely benign (Sep 22, 2018)
2-1635154-T-C			Benign (Sep 22, 2018)
2-1635185-G-C			Likely benign (Dec 24, 2019)
2-1635187-GT-G			Benign (Jul 27, 2018)
2-1635241-C-T			Benign (Aug 14, 2018)
2-1635288-A-G			Benign (Jul 27, 2018)
2-1635350-T-C			Benign (Jul 27, 2018)
2-1635398-C-T		Anterior segment dysgenesis 7	Likely benign (Aug 20, 2023)
2-1635409-T-C		PXDN-related disorder	Uncertain significance (May 03, 2024)
2-1635435-T-C		Anterior segment dysgenesis 7	Benign (Jan 20, 2024)
2-1635473-C-T		Inborn genetic diseases	Uncertain significance (May 27, 2022)
2-1635502-C-CGTGATTCAAG		Anterior segment dysgenesis 7	Pathogenic (Jul 19, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXDN	protein_coding	protein_coding	ENST00000252804	23	112966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.51e-7	1.00	124669	0	41	124710	0.000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	752	943	0.798	0.0000658	9601
Missense in Polyphen		227	347.29	0.65364		3585
Synonymous	-1.69	465	421	1.10	0.0000345	2969
Loss of Function	4.62	23	62.3	0.369	0.00000325	673

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000936	0.0000933
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.000225	0.000223
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000233	0.000230
Middle Eastern	0.000225	0.000223
South Asian	0.000202	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays low peroxidase activity and is likely to participate in H(2)O(2) metabolism and peroxidative reactions in the cardiovascular system. Plays a role in extracellular matrix formation. {ECO:0000269|PubMed:18929642, ECO:0000269|PubMed:19590037}.
• Disease: DISEASE: Anterior segment dysgenesis 7 (ASGD7) [MIM:269400]: A form of anterior segment dysgenesis, a group of defects affecting anterior structures of the eye including cornea, iris, lens, trabecular meshwork, and Schlemm canal. Anterior segment dysgeneses result from abnormal migration or differentiation of the neural crest derived mesenchymal cells that give rise to components of the anterior chamber during eye development. Different anterior segment anomalies may exist alone or in combination, including iris hypoplasia, enlarged or reduced corneal diameter, corneal vascularization and opacity, posterior embryotoxon, corectopia, polycoria, abnormal iridocorneal angle, ectopia lentis, and anterior synechiae between the iris and posterior corneal surface. Clinical conditions falling within the phenotypic spectrum of anterior segment dysgeneses include aniridia, Axenfeld anomaly, Reiger anomaly/syndrome, Peters anomaly, and iridogoniodysgenesis. ASGD7 is an autosomal recessive disease. {ECO:0000269|PubMed:21907015}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;EGF-EGFR Signaling Pathway;Crosslinking of collagen fibrils;Assembly of collagen fibrils and other multimeric structures;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -1.51
• rvis_percentile_EVS: 3.48

Haploinsufficiency Scores

• pHI: 0.443
• hipred: Y
• hipred_score: 0.685
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.267

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pxdn
• Phenotype: cellular phenotype; pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Zebrafish Information Network

• Gene name: pxdn
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved dorsal

Gene ontology

• Biological process: negative regulation of cytokine-mediated signaling pathway;immune response;response to oxidative stress;extracellular matrix organization;hydrogen peroxide catabolic process;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: peroxidase activity;interleukin-1 receptor antagonist activity;extracellular matrix structural constituent;heme binding;metal ion binding