LTO1

LTO1 maturation factor of ABCE1

Basic information

Region (hg38): 11:69653075-69675416

Previous symbols: [ "ORAOV1" ]

Links

ENSG00000149716 ∙ NCBI:220064 ∙ OMIM:607224 ∙ HGNC:17589 ∙ Uniprot:Q8WV07 ∙ 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 LTO1 gene.

• not provided (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTO1 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				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	0	1	0

Variants in LTO1

This is a list of pathogenic ClinVar variants found in the LTO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-69667530-G-A		not specified	Uncertain significance (Dec 30, 2023)
11-69667533-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-69667550-A-G		not specified	Uncertain significance (Feb 10, 2022)
11-69667580-G-A		not specified	Uncertain significance (Feb 21, 2024)
11-69667927-C-T		not specified	Uncertain significance (Jan 08, 2024)
11-69671762-T-C		not specified	Uncertain significance (Sep 15, 2021)
11-69671804-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-69671809-T-C		not specified	Uncertain significance (Aug 12, 2022)
11-69671823-T-G			Benign (Nov 03, 2017)
11-69673244-G-A		not specified	Uncertain significance (Jul 27, 2022)
11-69673271-C-A		not specified	Uncertain significance (Sep 01, 2021)
11-69673301-C-T		not specified	Likely benign (Apr 11, 2023)
11-69673302-G-A		not specified	Uncertain significance (Dec 26, 2023)
11-69673310-T-C		not specified	Uncertain significance (Aug 02, 2022)
11-69675235-G-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTO1	protein_coding	protein_coding	ENST00000279147	5	22341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00181	0.735	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.411	84	74.1	1.13	0.00000379	910
Missense in Polyphen		13	16.627	0.78184		201
Synonymous	0.760	23	28.1	0.818	0.00000166	228
Loss of Function	0.859	5	7.55	0.663	3.17e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000336	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The complex LTO1:YAE1 functions as a target specific adapter that probably recruits apo-ABCE1 to the cytosolic iron- sulfur protein assembly (CIA) complex machinery (PubMed:26182403). May be required for biogenesis of the large ribosomal subunit and initiation of translation (PubMed:23318452). May play a role in the regulation of proline metabolism and ROS production (PubMed:24930674). {ECO:0000269|PubMed:23318452, ECO:0000269|PubMed:24930674, ECO:0000269|PubMed:26182403}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.352
• ghis: 0.559

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: LTO1

Gene ontology

• Biological process: telomere maintenance;translational initiation;ribosomal large subunit biogenesis;protein maturation by [4Fe-4S] cluster transfer
• Cellular component: cellular_component;nucleus
• Molecular function: molecular_function;protein binding