PRXL2A

peroxiredoxin like 2A

Basic information

Region (hg38): 10:80407829-80437115

Previous symbols: [ "C10orf58", "FAM213A" ]

Links

ENSG00000122378 ∙ NCBI:84293 ∙ OMIM:617165 ∙ HGNC:28651 ∙ Uniprot:Q9BRX8 ∙ 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 PRXL2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRXL2A 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in PRXL2A

This is a list of pathogenic ClinVar variants found in the PRXL2A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-80420507-A-G		not specified	Uncertain significance (Jul 30, 2023)
10-80420518-T-G		not specified	Uncertain significance (Dec 21, 2022)
10-80420537-G-A		not specified	Uncertain significance (Nov 13, 2024)
10-80420548-G-C		not specified	Uncertain significance (Oct 22, 2021)
10-80422476-G-A		not specified	Uncertain significance (Dec 21, 2023)
10-80425873-C-T		not specified	Uncertain significance (Jan 09, 2024)
10-80425892-A-C		not specified	Uncertain significance (Dec 28, 2022)
10-80425914-G-A		not specified	Uncertain significance (Nov 06, 2023)
10-80427380-A-T		not specified	Uncertain significance (Apr 24, 2023)
10-80427392-G-A		not specified	Uncertain significance (Sep 12, 2023)
10-80427422-G-A		not specified	Uncertain significance (Nov 15, 2024)
10-80427437-A-T		not specified	Uncertain significance (Jul 19, 2022)
10-80427439-C-G		not specified	Uncertain significance (Feb 28, 2024)
10-80431986-G-A		not specified	Uncertain significance (Aug 04, 2024)
10-80432003-C-G		not specified	Uncertain significance (Jul 25, 2023)
10-80432012-A-C		not specified	Uncertain significance (Oct 21, 2024)
10-80432092-A-G		not specified	Uncertain significance (Nov 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRXL2A	protein_coding	protein_coding	ENST00000372181	5	25169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-10	0.0359	125695	1	52	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.611	107	126	0.847	0.00000666	1490
Missense in Polyphen		27	37.202	0.72577		414
Synonymous	-0.0815	50	49.3	1.01	0.00000272	457
Loss of Function	-0.417	14	12.4	1.13	7.64e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000817	0.000784
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in redox regulation of the cell (PubMed:26438880, PubMed:19951071). Acts as an antioxidant (PubMed:19951071, PubMed:26438880). Inhibits TNFSF11-induced NFKB1 and JUN activation and osteoclast differentiation (PubMed:19951071). May affect bone resorption and help to maintain bone mass (PubMed:19951071). Acts as a negative regulator of macrophage-mediated inflammation by inhibiting macrophage production of inflammatory cytokines, probably through suppression of the MAPK signaling pathway (PubMed:26438880). {ECO:0000269|PubMed:19951071, ECO:0000269|PubMed:26438880}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.205
• ghis: 0.489

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Fam213a
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: regulation of osteoclast differentiation;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: extracellular region;cytoplasm
• Molecular function: antioxidant activity