LTV1

LTV1 ribosome biogenesis factor, the group of SSU processome

Basic information

Region (hg38): 6:143843337-143863812

Previous symbols: [ "C6orf93" ]

Links

ENSG00000135521 ∙ NCBI:84946 ∙ OMIM:620074 ∙ HGNC:21173 ∙ Uniprot:Q96GA3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inflammatory poikiloderma with hair abnormalities and acral keratoses (Limited), mode of inheritance: AR
• inflammatory poikiloderma with hair abnormalities and acral keratoses (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Inflammatory poikiloderma with hair abnormalities and acral keratoses	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	34999892

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LTV1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTV1 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					2	2
missense			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	3

Variants in LTV1

This is a list of pathogenic ClinVar variants found in the LTV1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-143844568-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-143844595-G-T		not specified	Uncertain significance (May 17, 2023)
6-143846072-G-A		not specified	Uncertain significance (Apr 01, 2024)
6-143846117-T-A		not specified	Uncertain significance (Jan 26, 2022)
6-143846133-A-G		not specified	Uncertain significance (Jun 18, 2021)
6-143857362-G-A		not specified	Uncertain significance (Jun 12, 2023)
6-143857380-C-T		not specified	Uncertain significance (Dec 13, 2023)
6-143857408-A-G		Inflammatory poikiloderma with hair abnormalities and acral keratoses	Pathogenic (Jan 11, 2023)
6-143857799-A-T		not specified	Uncertain significance (Feb 10, 2023)
6-143857802-A-C		not specified	Uncertain significance (Jul 25, 2023)
6-143857802-A-G		not specified	Uncertain significance (Jan 16, 2024)
6-143857832-C-A		not specified	Uncertain significance (Dec 15, 2022)
6-143857928-G-A		not specified	Uncertain significance (May 24, 2024)
6-143857936-G-A		not specified	Uncertain significance (Oct 26, 2022)
6-143857991-A-T		not specified	Uncertain significance (Aug 12, 2022)
6-143860512-A-G			Benign (Mar 29, 2018)
6-143860538-A-T		not specified	Uncertain significance (May 23, 2023)
6-143862132-T-C			Benign (Mar 29, 2018)
6-143862211-C-T		not specified	Uncertain significance (Jun 30, 2022)
6-143862213-A-G		not specified	Uncertain significance (Apr 26, 2023)
6-143862214-A-G			Benign (Mar 29, 2018)
6-143863099-G-A		not specified	Likely benign (Feb 16, 2023)
6-143863165-C-T		not specified	Uncertain significance (Mar 23, 2022)
6-143863174-T-C		not specified	Uncertain significance (Feb 21, 2024)
6-143863225-C-G		not specified	Uncertain significance (Mar 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTV1	protein_coding	protein_coding	ENST00000367576	11	20469

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.58e-8	0.971	125541	0	207	125748	0.000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.439	225	244	0.921	0.0000119	3158
Missense in Polyphen		71	86.013	0.82545		1079
Synonymous	0.962	76	87.4	0.869	0.00000429	827
Loss of Function	2.10	16	28.0	0.572	0.00000159	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00111
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00121	0.00120
Middle Eastern	0.000326	0.000326
South Asian	0.000785	0.000784
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.317
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.0836
• hipred: Y
• hipred_score: 0.610
• ghis: 0.544

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ltv1

Zebrafish Information Network

• Gene name: ltv1
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased width

Gene ontology

• Biological process: ribosomal small subunit export from nucleus;ribosomal small subunit biogenesis
• Cellular component: nucleus;nucleoplasm;cytosol;preribosome, small subunit precursor;late endosome membrane;EGO complex
• Molecular function: protein binding