LONRF2

LON peptidase N-terminal domain and ring finger 2, the group of Ring finger proteins

Basic information

Region (hg38): 2:100271875-100322501

Links

ENSG00000170500 ∙ NCBI:164832 ∙ ∙ HGNC:24788 ∙ Uniprot:Q1L5Z9 ∙ 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 LONRF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LONRF2 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	2
missense			41	3		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	4	1

Variants in LONRF2

This is a list of pathogenic ClinVar variants found in the LONRF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-100284335-C-T		not specified	Uncertain significance (Feb 21, 2024)
2-100284350-C-T		not specified	Uncertain significance (May 27, 2022)
2-100284404-G-T		not specified	Uncertain significance (May 11, 2022)
2-100284408-T-C		not specified	Uncertain significance (Oct 05, 2023)
2-100284417-T-C		not specified	Uncertain significance (Oct 12, 2022)
2-100284434-C-T		not specified	Uncertain significance (Jan 03, 2022)
2-100284451-G-A			Likely benign (Dec 01, 2022)
2-100286918-G-A		not specified	Uncertain significance (Aug 10, 2021)
2-100286957-A-G		not specified	Uncertain significance (Sep 14, 2022)
2-100286962-T-A		not specified	Uncertain significance (Jul 19, 2023)
2-100286975-C-T		not specified	Likely benign (May 17, 2023)
2-100286976-G-A		not specified	Uncertain significance (Nov 08, 2021)
2-100290335-T-C		not specified	Uncertain significance (Oct 06, 2021)
2-100290347-C-A		not specified	Uncertain significance (Oct 17, 2023)
2-100290413-C-G		not specified	Uncertain significance (Dec 03, 2021)
2-100295468-T-C		not specified	Uncertain significance (Nov 10, 2022)
2-100295489-G-A		not specified	Uncertain significance (Feb 06, 2023)
2-100295518-C-T			Benign (Dec 31, 2019)
2-100298868-G-T			Likely benign (Mar 01, 2023)
2-100299740-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-100299791-C-T		not specified	Uncertain significance (Jan 20, 2023)
2-100299849-G-A		not specified	Uncertain significance (Oct 10, 2023)
2-100299878-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-100299881-T-C		not specified	Uncertain significance (Aug 08, 2022)
2-100299893-A-G		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LONRF2	protein_coding	protein_coding	ENST00000393437	12	49443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00117	0.998	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	248	357	0.694	0.0000200	4756
Missense in Polyphen		47	96.397	0.48757		1227
Synonymous	0.706	133	144	0.925	0.00000874	1510
Loss of Function	3.10	10	27.6	0.362	0.00000132	386

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000109	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.179
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.99

Haploinsufficiency Scores

• pHI: 0.0676
• hipred: Y
• hipred_score: 0.659
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.522

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lonrf2

Gene ontology

• Molecular function: metal ion binding