PXDNL

peroxidasin like, the group of I-set domain containing

Basic information

Region (hg38): 8:51319577-51809445

Links

ENSG00000147485 ∙ NCBI:137902 ∙ OMIM:615904 ∙ HGNC:26359 ∙ Uniprot:A1KZ92 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXDNL 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				13	10	23
missense			92	11	21	124
nonsense					1	1
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region				1	1	2
non coding					3	3
Total	0	0	92	24	37

Variants in PXDNL

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

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

Position	Type	Phenotype	Significance	ClinVar
8-51319895-C-T		not specified	Uncertain significance (Apr 20, 2024)
8-51319919-A-C		not specified	Uncertain significance (Sep 22, 2023)
8-51319927-G-T		PXDNL-related disorder	Benign (Oct 28, 2019)
8-51319952-C-T		not specified	Uncertain significance (Feb 28, 2023)
8-51319982-G-A		not specified	Uncertain significance (Sep 17, 2021)
8-51319989-G-A		not specified	Uncertain significance (Apr 05, 2023)
8-51319994-A-C		not specified	Uncertain significance (Dec 21, 2022)
8-51320805-G-A		PXDNL-related disorder	Benign (May 21, 2018)
8-51320821-C-T		not specified	Likely benign (Aug 26, 2022)
8-51320828-C-T		not specified	Uncertain significance (Jun 23, 2021)
8-51320847-T-G		not specified	Uncertain significance (Oct 10, 2023)
8-51320848-C-T		PXDNL-related disorder	Benign (Oct 28, 2019)
8-51320854-T-C		not specified	Uncertain significance (Sep 27, 2022)
8-51320856-T-C			Likely benign (Mar 01, 2023)
8-51320895-T-C		not specified	Uncertain significance (Aug 20, 2023)
8-51339633-G-T		PXDNL-related disorder	Benign (Aug 20, 2019)
8-51339745-T-G		PXDNL-related disorder	Benign (Dec 31, 2019)
8-51339751-T-A		not specified	Uncertain significance (Apr 18, 2023)
8-51339760-A-G		PXDNL-related disorder	Benign (Oct 28, 2019)
8-51345869-A-T		PXDNL-related disorder	Benign (Feb 14, 2020)
8-51345873-G-A		not specified	Uncertain significance (Apr 16, 2024)
8-51345878-C-A		not specified	Uncertain significance (Apr 26, 2024)
8-51345894-G-A		not specified	Uncertain significance (Oct 20, 2023)
8-51345934-T-A		PXDNL-related disorder	Likely benign (Mar 01, 2022)
8-51371877-A-C		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXDNL	protein_coding	protein_coding	ENST00000356297	23	489868

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.20e-35	0.000245	119322	112	5236	124670	0.0217

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.197	840	824	1.02	0.0000493	9417
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0450	0.0446
Ashkenazi Jewish	0.0431	0.0427
East Asian	0.00164	0.00161
Finnish	0.00451	0.00447
European (Non-Finnish)	0.0166	0.0164
Middle Eastern	0.00164	0.00161
South Asian	0.0693	0.0683
Other	0.0169	0.0165

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.177
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0943

Gene Damage Prediction

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

Gene ontology

• Biological process: response to oxidative stress;hydrogen peroxide catabolic process;oxidation-reduction process;nucleic acid phosphodiester bond hydrolysis;cellular oxidant detoxification
• Cellular component: extracellular space;cytoplasm
• Molecular function: endonuclease activity;peroxidase activity;heme binding;metal ion binding