PYROXD2

pyridine nucleotide-disulphide oxidoreductase domain 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:98383564-98415182

Previous symbols: [ "C10orf33" ]

Links

ENSG00000119943 ∙ NCBI:84795 ∙ OMIM:617889 ∙ HGNC:23517 ∙ Uniprot:Q8N2H3 ∙ 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 PYROXD2 gene.

• Inborn genetic diseases (36 variants)
• Leigh syndrome (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 PYROXD2 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						0
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in PYROXD2

This is a list of pathogenic ClinVar variants found in the PYROXD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-98383818-T-C		not specified	Uncertain significance (Sep 06, 2022)
10-98385006-T-C		not specified	Uncertain significance (Aug 08, 2023)
10-98385015-A-G		not specified	Uncertain significance (Sep 01, 2021)
10-98385047-C-T		not specified	Uncertain significance (Jan 09, 2024)
10-98385048-A-G		not specified	Uncertain significance (Jul 14, 2023)
10-98385052-C-T		not specified	Uncertain significance (Dec 23, 2022)
10-98387250-T-C		not specified	Uncertain significance (Apr 08, 2022)
10-98387256-C-T		not specified	Uncertain significance (Nov 07, 2023)
10-98387268-T-A		not specified	Uncertain significance (Dec 05, 2022)
10-98387269-C-G		not specified	Uncertain significance (Dec 05, 2022)
10-98388376-C-A		not specified	Uncertain significance (Mar 25, 2022)
10-98388417-G-C		not specified	Uncertain significance (Oct 17, 2023)
10-98388441-C-T		not specified	Likely benign (Aug 02, 2022)
10-98388506-G-C		not specified	Uncertain significance (Sep 29, 2022)
10-98390611-G-C			Uncertain significance (Jan 01, 2023)
10-98390640-T-G		not specified	Uncertain significance (Dec 21, 2022)
10-98390641-G-A		not specified	Uncertain significance (Jan 29, 2024)
10-98390656-C-T		not specified	Uncertain significance (Jul 20, 2021)
10-98390685-T-C		not specified	Uncertain significance (Jun 09, 2022)
10-98390724-G-A		not specified	Uncertain significance (May 13, 2022)
10-98390737-G-A		not specified	Uncertain significance (Jan 30, 2024)
10-98391034-G-A		not specified	Uncertain significance (Sep 26, 2023)
10-98392430-A-C		Leigh syndrome	Uncertain significance (May 02, 2023)
10-98392439-G-A		not specified	Uncertain significance (Apr 08, 2022)
10-98392472-T-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYROXD2	protein_coding	protein_coding	ENST00000370575	16	31620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00e-15	0.0704	125294	1	453	125748	0.00181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.253	352	339	1.04	0.0000187	3733
Missense in Polyphen		70	70.301	0.99572		731
Synonymous	0.114	142	144	0.988	0.00000885	1203
Loss of Function	0.824	26	30.9	0.840	0.00000148	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0129	0.0125
Ashkenazi Jewish	0.00	0.00
East Asian	0.00299	0.00299
Finnish	0.0000478	0.0000462
European (Non-Finnish)	0.000636	0.000633
Middle Eastern	0.00299	0.00299
South Asian	0.000623	0.000621
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable oxidoreductase. {ECO:0000250}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.949
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.29

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.229
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.297

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pyroxd2

Gene ontology

• Biological process: oxidation-reduction process
• Molecular function: protein binding;oxidoreductase activity