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.

• not_specified (102 variants)

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. These statistics are base on transcript: NM_000152271.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			95	6		101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	95	7	0

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