LTN1

listerin E3 ubiquitin protein ligase 1, the group of Armadillo like helical domain containing|Ring finger proteins

Basic information

Region (hg38): 21:28928144-28992956

Previous symbols: [ "C21orf98", "C21orf10", "ZNF294", "RNF160" ]

Links

ENSG00000198862 ∙ NCBI:26046 ∙ OMIM:613083 ∙ HGNC:13082 ∙ Uniprot:O94822 ∙ 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 LTN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTN1 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				3		3
missense			66	5	2	73
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	8	2

Variants in LTN1

This is a list of pathogenic ClinVar variants found in the LTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-28931172-AT-A		Neurodevelopmental disorder	Uncertain significance (Jan 01, 2019)
21-28931273-T-C		not specified	Uncertain significance (Aug 01, 2022)
21-28936584-C-G		not specified	Uncertain significance (Jul 29, 2022)
21-28936658-T-C		not specified	Uncertain significance (Sep 25, 2023)
21-28936670-G-A		not specified	Uncertain significance (Sep 16, 2021)
21-28941250-T-C		not specified	Uncertain significance (Nov 17, 2022)
21-28941287-C-T		not specified	Uncertain significance (Aug 10, 2021)
21-28941372-T-C		not specified	Uncertain significance (Jul 19, 2023)
21-28943680-G-A		not specified	Uncertain significance (Jan 04, 2024)
21-28943746-T-C		not specified	Uncertain significance (Nov 20, 2023)
21-28944401-T-G		not specified	Likely benign (Mar 30, 2024)
21-28944435-A-C		not specified	Uncertain significance (Jun 29, 2023)
21-28944466-G-T		not specified	Uncertain significance (Dec 07, 2023)
21-28944472-T-C		not specified	Uncertain significance (Apr 09, 2024)
21-28944479-T-C		not specified	Likely benign (Aug 13, 2021)
21-28944525-C-G		not specified	Uncertain significance (Oct 30, 2023)
21-28944590-T-C		not specified	Uncertain significance (Mar 04, 2024)
21-28945865-G-A		not specified	Uncertain significance (Mar 21, 2022)
21-28945865-G-T		not specified	Uncertain significance (Aug 08, 2023)
21-28946215-T-C		not specified	Uncertain significance (Nov 08, 2022)
21-28946231-C-A		not specified	Uncertain significance (May 17, 2023)
21-28946239-C-T		not specified	Uncertain significance (Jun 06, 2023)
21-28952208-C-T		not specified	Uncertain significance (Oct 24, 2023)
21-28952236-G-A		not specified	Uncertain significance (Feb 16, 2023)
21-28953244-G-A		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTN1	protein_coding	protein_coding	ENST00000389194	30	64805

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00840	0.992	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	738	898	0.822	0.0000444	11841
Missense in Polyphen		170	277.49	0.61264		3717
Synonymous	0.404	319	328	0.972	0.0000165	3406
Loss of Function	6.38	22	85.8	0.256	0.00000431	1165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000273
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000333	0.000326
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000241	0.000229
Middle Eastern	0.000333	0.000326
South Asian	0.000147	0.000131
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23685075, PubMed:25132172, PubMed:25578875). Ubiquitination leads to VCP/p97 recruitment for extraction and degradation of the incomplete translation product (By similarity). {ECO:0000250|UniProtKB:Q04781, ECO:0000269|PubMed:23685075, ECO:0000269|PubMed:25132172, ECO:0000269|PubMed:25578875}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0993

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.630
• hipred: N
• hipred_score: 0.476
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ltn1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); muscle phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: proteasome-mediated ubiquitin-dependent protein catabolic process;protein autoubiquitination;rescue of stalled ribosome;ribosome-associated ubiquitin-dependent protein catabolic process
• Cellular component: cytosol;RQC complex
• Molecular function: protein binding;zinc ion binding;ribosomal large subunit binding;ubiquitin protein ligase activity