LONRF1

LON peptidase N-terminal domain and ring finger 1, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 8:12721906-12756073

Links

ENSG00000154359 ∙ NCBI:91694 ∙ ∙ HGNC:26302 ∙ Uniprot:Q17RB8 ∙ 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 LONRF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LONRF1 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			46	3		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	47	3	0

Variants in LONRF1

This is a list of pathogenic ClinVar variants found in the LONRF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-12723136-T-C		not specified	Uncertain significance (Dec 19, 2022)
8-12723181-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-12725854-T-C		not specified	Uncertain significance (May 25, 2022)
8-12725856-C-G		not specified	Uncertain significance (Jan 26, 2022)
8-12725857-T-C		not specified	Uncertain significance (Feb 21, 2024)
8-12725870-C-T		not specified	Uncertain significance (May 13, 2024)
8-12728927-C-T		not specified	Uncertain significance (Feb 10, 2023)
8-12728959-T-C		not specified	Uncertain significance (Nov 23, 2022)
8-12728996-C-A		not specified	Uncertain significance (May 01, 2022)
8-12729056-C-T		not specified	Uncertain significance (Jan 11, 2023)
8-12729224-T-C		not specified	Uncertain significance (Nov 27, 2023)
8-12731758-C-T		not specified	Uncertain significance (Oct 06, 2022)
8-12731761-C-T		not specified	Uncertain significance (Nov 23, 2021)
8-12731782-A-T		not specified	Uncertain significance (Sep 17, 2021)
8-12736767-A-G		not specified	Uncertain significance (May 10, 2022)
8-12736788-T-A		not specified	Uncertain significance (Feb 03, 2022)
8-12737017-A-G		not specified	Uncertain significance (Jan 19, 2022)
8-12737110-G-A		not specified	Uncertain significance (Mar 01, 2024)
8-12737123-C-G		not specified	Uncertain significance (Feb 22, 2024)
8-12738013-A-T		not specified	Uncertain significance (Jun 22, 2023)
8-12738014-T-C		not specified	Likely benign (Mar 16, 2024)
8-12738066-T-C		not specified	Uncertain significance (May 30, 2023)
8-12738105-C-T		not specified	Uncertain significance (Dec 27, 2023)
8-12740879-G-C		not specified	Likely benign (Dec 28, 2023)
8-12740952-T-G		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LONRF1	protein_coding	protein_coding	ENST00000398246	12	34180

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.612	0.388	124779	0	15	124794	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.375	303	322	0.941	0.0000160	4904
Missense in Polyphen		71	145.38	0.48837		2016
Synonymous	-1.70	145	121	1.20	0.00000643	1542
Loss of Function	4.26	7	33.6	0.208	0.00000165	468

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000944	0.0000944
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000805	0.0000794
Middle Eastern	0.00	0.00
South Asian	0.0000356	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.101

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.501
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lonrf1

Gene ontology

• Biological process: protein polyubiquitination
• Cellular component: cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding