LONP2

lon peptidase 2, peroxisomal, the group of AAA ATPases

Basic information

Region (hg38): 16:48244299-48363122

Links

ENSG00000102910 ∙ NCBI:83752 ∙ OMIM:617774 ∙ HGNC:20598 ∙ Uniprot:Q86WA8 ∙ 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 LONP2 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LONP2 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			18	1		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	18	1	0

Variants in LONP2

This is a list of pathogenic ClinVar variants found in the LONP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-48244422-C-T		not specified	Uncertain significance (Aug 08, 2023)
16-48244604-C-A		not specified	Uncertain significance (Oct 13, 2023)
16-48252309-A-G		not specified	Uncertain significance (Jan 18, 2022)
16-48252360-G-A		not specified	Uncertain significance (Aug 02, 2022)
16-48256612-G-T		Malignant tumor of prostate	Uncertain significance (-)
16-48258634-G-A		not specified	Uncertain significance (Feb 17, 2024)
16-48261436-C-T		not specified	Uncertain significance (Apr 08, 2022)
16-48261459-T-G		not specified	Uncertain significance (Jan 23, 2024)
16-48261571-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-48262783-A-G		not specified	Uncertain significance (Aug 09, 2021)
16-48262788-A-G		not specified	Uncertain significance (May 23, 2023)
16-48262840-T-C		not specified	Uncertain significance (Nov 21, 2022)
16-48270018-C-T		not specified	Uncertain significance (Jan 26, 2023)
16-48270019-G-A		not specified	Uncertain significance (Feb 21, 2024)
16-48277456-G-T		not specified	Uncertain significance (Jan 19, 2022)
16-48303212-C-G		not specified	Uncertain significance (Jun 05, 2023)
16-48303301-A-T		not specified	Uncertain significance (Nov 08, 2021)
16-48347578-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-48347698-G-T		not specified	Uncertain significance (Dec 09, 2023)
16-48348135-A-G		not specified	Uncertain significance (Sep 25, 2023)
16-48348214-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-48351600-A-G		not specified	Uncertain significance (May 30, 2023)
16-48351635-G-A		not specified	Likely benign (Jun 22, 2021)
16-48351681-G-C		not specified	Uncertain significance (May 09, 2023)
16-48351755-G-A		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LONP2	protein_coding	protein_coding	ENST00000285737	15	118827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.24e-28	0.0000692	125495	0	253	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	337	474	0.711	0.0000252	5530
Missense in Polyphen		119	197.98	0.60108		2195
Synonymous	1.12	153	172	0.891	0.00000885	1728
Loss of Function	-0.233	41	39.4	1.04	0.00000232	457

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00186	0.00185
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000220	0.000217
Finnish	0.000323	0.000323
European (Non-Finnish)	0.00132	0.00132
Middle Eastern	0.000220	0.000217
South Asian	0.000968	0.000915
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP-dependent serine protease that mediates the selective degradation of misfolded and unassembled polypeptides in the peroxisomal matrix. Necessary for type 2 peroxisome targeting signal (PTS2)-containing protein processing and facilitates peroxisome matrix protein import (By similarity). May indirectly regulate peroxisomal fatty acid beta-oxidation through degradation of the self-processed forms of TYSND1. {ECO:0000255|HAMAP- Rule:MF_03121, ECO:0000269|PubMed:22002062}.
• Pathway: Metabolism of proteins;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Peroxisomal protein import;Protein folding (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.868
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.0654
• hipred: N
• hipred_score: 0.379
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lonp2

Gene ontology

• Biological process: protein quality control for misfolded or incompletely synthesized proteins;protein targeting to peroxisome;peroxisome organization;response to organic cyclic compound;protein processing;protein import into peroxisome matrix;regulation of fatty acid beta-oxidation
• Cellular component: nucleus;peroxisome;peroxisomal matrix;cytosol;membrane
• Molecular function: protease binding;ATP-dependent peptidase activity;serine-type endopeptidase activity;signaling receptor binding;protein binding;ATP binding;peptidase activity;enzyme binding