PXMP4

peroxisomal membrane protein 4, the group of Tim17 family

Basic information

Region (hg38): 20:33702758-33720319

Links

ENSG00000101417 ∙ NCBI:11264 ∙ OMIM:616397 ∙ HGNC:15920 ∙ Uniprot:Q9Y6I8 ∙ 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 PXMP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXMP4 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	2		19
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	2	0

Variants in PXMP4

This is a list of pathogenic ClinVar variants found in the PXMP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33707720-G-C		not specified	Uncertain significance (Mar 31, 2023)
20-33707753-C-T		not specified	Uncertain significance (Jan 18, 2022)
20-33707754-G-T		not specified	Uncertain significance (Jun 22, 2023)
20-33707762-C-T		not specified	Uncertain significance (Feb 17, 2023)
20-33707782-T-C		not specified	Uncertain significance (Mar 29, 2023)
20-33707846-C-A		not specified	Uncertain significance (Jun 18, 2024)
20-33707863-G-A		not specified	Uncertain significance (Dec 13, 2022)
20-33707894-G-A		not specified	Uncertain significance (Aug 22, 2022)
20-33710604-A-G		not specified	Uncertain significance (Aug 12, 2021)
20-33710691-C-T		not specified	Uncertain significance (May 25, 2022)
20-33710692-G-A		not specified	Likely benign (Mar 08, 2024)
20-33710716-A-C		not specified	Uncertain significance (Feb 01, 2023)
20-33710737-A-G		not specified	Likely benign (Apr 04, 2023)
20-33710744-C-G		not specified	Uncertain significance (Sep 25, 2023)
20-33710746-C-T		not specified	Uncertain significance (Jul 21, 2021)
20-33714683-C-T		not specified	Uncertain significance (May 24, 2023)
20-33714690-G-A		not specified	Uncertain significance (Aug 12, 2021)
20-33714707-G-A		not specified	Uncertain significance (Nov 18, 2022)
20-33720120-G-A		not specified	Uncertain significance (Feb 06, 2024)
20-33720152-C-G		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXMP4	protein_coding	protein_coding	ENST00000409299	4	13614

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000759	0.782	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	109	133	0.820	0.00000792	1353
Missense in Polyphen		34	44.879	0.7576		461
Synonymous	0.348	57	60.4	0.943	0.00000374	458
Loss of Function	1.04	6	9.46	0.635	4.89e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00130	0.00129
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000435	0.000435
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Peroxisome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.314
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.425
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.532

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pxmp4

Gene ontology

• Biological process: biological_process
• Cellular component: peroxisome;peroxisomal membrane;integral component of membrane
• Molecular function: protein binding