PXMP2

peroxisomal membrane protein 2

Basic information

Region (hg38): 12:132687587-132704985

Links

ENSG00000176894 ∙ NCBI:5827 ∙ OMIM:617399 ∙ HGNC:9716 ∙ Uniprot:Q9NR77 ∙ 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 PXMP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXMP2 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		1
missense			20	2		22
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	1

Variants in PXMP2

This is a list of pathogenic ClinVar variants found in the PXMP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-132687678-C-T			Likely benign (Jul 14, 2018)
12-132687684-C-T		not specified	Uncertain significance (Jun 13, 2024)
12-132687692-C-G		not specified	Uncertain significance (Jan 16, 2025)
12-132687698-G-T		not specified	Uncertain significance (Mar 21, 2023)
12-132687709-G-C			Likely benign (Jul 01, 2022)
12-132687747-T-C		not specified	Uncertain significance (Nov 08, 2022)
12-132687768-C-T		not specified	Uncertain significance (Jul 09, 2021)
12-132687770-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-132690312-A-G		not specified	Uncertain significance (Oct 12, 2021)
12-132690336-A-C		not specified	Uncertain significance (Jan 03, 2024)
12-132690352-G-T		not specified	Uncertain significance (Aug 05, 2024)
12-132690362-A-T		not specified	Uncertain significance (Jan 01, 2025)
12-132690375-G-A		not specified	Uncertain significance (May 03, 2023)
12-132695960-G-C		not specified	Uncertain significance (Feb 24, 2025)
12-132695987-C-T		not specified	Uncertain significance (Jul 10, 2024)
12-132695993-G-A		not specified	Uncertain significance (Nov 21, 2024)
12-132701260-C-T		not specified	Uncertain significance (Aug 19, 2024)
12-132701274-G-A		not specified	Likely benign (Oct 06, 2021)
12-132701277-A-G		not specified	Uncertain significance (Mar 24, 2023)
12-132701283-A-AG			Benign (Aug 20, 2018)
12-132701302-C-T		not specified	Uncertain significance (Oct 09, 2024)
12-132701319-C-T		not specified	Uncertain significance (May 30, 2024)
12-132704623-G-A		not specified	Uncertain significance (Nov 19, 2024)
12-132704634-G-A		not specified	Uncertain significance (Oct 19, 2024)
12-132704638-A-G		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXMP2	protein_coding	protein_coding	ENST00000317479	5	33085

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00918	0.823	124519	12	1217	125748	0.00490

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.495	113	99.1	1.14	0.00000603	1228
Missense in Polyphen		32	29.007	1.1032		348
Synonymous	0.475	40	44.0	0.909	0.00000296	404
Loss of Function	1.10	4	7.17	0.558	3.05e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00337	0.00336
Ashkenazi Jewish	0.0105	0.0105
East Asian	0.000496	0.000489
Finnish	0.00257	0.00254
European (Non-Finnish)	0.00292	0.00290
Middle Eastern	0.000496	0.000489
South Asian	0.0205	0.0201
Other	0.00594	0.00588

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the peroxisomal membrane.
• Pathway: Peroxisome - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Metabolism of amino acids and derivatives;Metabolism;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Glyoxylate metabolism and glycine degradation;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.327
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.201
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pxmp2
• Phenotype: reproductive system phenotype; liver/biliary system phenotype; renal/urinary system 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: cytoplasm;peroxisomal membrane;membrane;integral component of membrane;protein-containing complex
• Molecular function: protein binding