LONRF3

LON peptidase N-terminal domain and ring finger 3, the group of Ring finger proteins

Basic information

Region (hg38): X:118974614-119022925

Previous symbols: [ "RNF127" ]

Links

ENSG00000175556 ∙ NCBI:79836 ∙ ∙ HGNC:21152 ∙ Uniprot:Q496Y0 ∙ 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 LONRF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LONRF3 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				4		4
missense			30	2		32
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	30	7	0

Variants in LONRF3

This is a list of pathogenic ClinVar variants found in the LONRF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-118974796-A-G		not specified	Uncertain significance (Nov 04, 2023)
X-118974819-C-T		not specified	Likely benign (Oct 31, 2023)
X-118974848-C-T		not specified	Likely benign (Dec 26, 2023)
X-118974890-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-118974895-C-A		not specified	Uncertain significance (Nov 09, 2021)
X-118974900-G-T		not specified	Uncertain significance (Jul 12, 2023)
X-118974911-A-T		not specified	Uncertain significance (Dec 14, 2023)
X-118974919-G-T		not specified	Uncertain significance (Apr 22, 2022)
X-118974920-C-A		not specified	Uncertain significance (Dec 27, 2023)
X-118975022-G-A			Uncertain significance (Sep 07, 2022)
X-118975058-T-C		not specified	Uncertain significance (Jul 25, 2023)
X-118975078-G-A		not specified	Uncertain significance (Oct 27, 2021)
X-118975168-A-G		not specified	Uncertain significance (Jun 09, 2022)
X-118975243-G-T		not specified	Uncertain significance (Nov 27, 2023)
X-118975342-G-T		not specified	Uncertain significance (May 06, 2024)
X-118975349-G-A		not specified	Uncertain significance (May 18, 2023)
X-118975381-G-C		not specified	Uncertain significance (Mar 11, 2024)
X-118975393-G-A		not specified	Uncertain significance (May 30, 2023)
X-118975408-C-G		not specified	Uncertain significance (Feb 13, 2024)
X-118975471-G-A		not specified	Uncertain significance (Sep 28, 2022)
X-118978362-C-T		not specified	Uncertain significance (May 21, 2024)
X-118987026-C-T			Likely benign (Oct 01, 2022)
X-118989421-T-C			Likely benign (Mar 01, 2023)
X-118989562-C-T		not specified	Uncertain significance (Jun 10, 2024)
X-118989579-A-G		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LONRF3	protein_coding	protein_coding	ENST00000371628	11	43738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.418	0.582	125686	1	3	125690	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	224	284	0.788	0.0000212	4901
Missense in Polyphen		73	138.15	0.5284		2294
Synonymous	-0.518	122	115	1.06	0.00000870	1506
Loss of Function	3.44	5	22.7	0.220	0.00000160	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000450	0.0000450
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000275	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000226	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.214
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.516
• hipred: Y
• hipred_score: 0.563
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0493

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lonrf3
• Phenotype: immune system phenotype; skeleton phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Molecular function: protein binding;metal ion binding