PXDNL

protein-coding

peroxidasin like, the group of I-set domain containing

Gene summary

Predicted to enable heme binding activity and peroxidase activity. Predicted to be involved in hydrogen peroxide catabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_144651.5

Inheritance

—

ClinVar variants

U:261B:56

Top phenotype

PXDNL-related disorder

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr8:51,319,577-51,809,445

External References & Databases

Ensembl (ENSG00000147485)

Transcript & Mutation Effects

hg38 • Region Span ~489.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PXDNL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 263

PXDNL-related disorderTotal: 38

not providedTotal: 31

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144651.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	12 clinvar	7 clinvar	21
missense			256 clinvar	20 clinvar	14 clinvar	290
nonsense			2 clinvar		1 clinvar	3
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			1 clinvar		1 clinvar	2
Total	0	0	261	32	24	317

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144651.5	RefSeq	NP_653252.4	23	MANE Select
ENST00000356297.5	Ensembl	ENSP00000348645.4	23	MANE Select
ENST00000522628.5	Ensembl	ENSP00000429855.1	4	Standard
ENST00000522933.5	Ensembl	ENSP00000428114.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to oxidative stress
hydrogen peroxide catabolic process
oxidation-reduction process
nucleic acid phosphodiester bond hydrolysis
cellular oxidant detoxification

Molecular Function

endonuclease activity
peroxidase activity
heme binding
metal ion binding

Cellular Component

extracellular space
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356297
Coding exons: 23
Length: 489868
Individuals with no LoFs: 119322
Homozygous LoFs: 112
Heterozygous LoFs: 5236
Defined: 124670
p: 0.0217

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.197	840	824	1.02	0.0000493	9417
Missense (PolyPhen)		289	274.21	1.0539		3355
Synonymous	1.27	310	340	0.913	0.0000229	2914
Loss of Function	0.929	58	66.2	0.877	0.00000377	733

Population LoF Frequency

Population	CAF	p-value	Status
African	0.036	0.036	notable
Latino/Admixed American	0.0089	0.0088	notable
Ashkenazi Jewish	0.043	0.043	notable
East Asian	0.0016	0.0016	notable
Finnish	0.0045	0.0045	notable
European (Non-Finnish)	0.017	0.016	notable
South Asian	0.069	0.068	notable
Other	0.017	0.016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Isoform PMR1: Endonuclease selectively degrading some target mRNAs while they are engaged by translating ribosomes, among which albumin and beta-globin mRNAs. {ECO:0000269|PubMed:22543864}.;

Intolerance Scores

RVIS EVS: 2.73
RVIS percentile EVS: 98.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0943

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High