L1TD1

LINE1 type transposase domain containing 1

Basic information

Region (hg38): 1:62194790-62235060

Links

ENSG00000240563 ∙ NCBI:54596 ∙ ∙ HGNC:25595 ∙ Uniprot:Q5T7N2 ∙ 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 L1TD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the L1TD1 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				1		1
missense			27	2		29
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	27	3	1

Variants in L1TD1

This is a list of pathogenic ClinVar variants found in the L1TD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-62206796-G-C		not specified	Uncertain significance (Oct 25, 2023)
1-62206830-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-62206854-G-A		not specified	Uncertain significance (May 14, 2024)
1-62206875-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-62206885-C-T		not specified	Uncertain significance (Jun 16, 2023)
1-62206995-A-C		not specified	Uncertain significance (Nov 12, 2021)
1-62207090-T-G		not specified	Likely benign (Mar 31, 2023)
1-62207092-A-G		not specified	Uncertain significance (Mar 07, 2024)
1-62207110-C-A		not specified	Uncertain significance (Apr 08, 2024)
1-62207140-T-C		not specified	Uncertain significance (Nov 18, 2022)
1-62207161-T-C		not specified	Uncertain significance (Jul 05, 2022)
1-62209885-A-G		not specified	Uncertain significance (Oct 03, 2022)
1-62209965-T-A		not specified	Uncertain significance (Mar 02, 2023)
1-62209976-C-T		not specified	Uncertain significance (May 04, 2022)
1-62210059-G-T		not specified	Uncertain significance (Oct 25, 2022)
1-62210074-G-A		not specified	Uncertain significance (Jan 20, 2023)
1-62210137-A-G		not specified	Uncertain significance (Oct 25, 2022)
1-62210140-C-T		not specified	Uncertain significance (May 29, 2024)
1-62210284-C-G		not specified	Uncertain significance (Aug 02, 2021)
1-62210335-A-G		not specified	Uncertain significance (Feb 13, 2024)
1-62210359-G-C		not specified	Uncertain significance (Mar 29, 2023)
1-62210363-A-C		not specified	Uncertain significance (Dec 16, 2023)
1-62210364-C-T			Likely benign (Sep 01, 2022)
1-62210374-G-A		not specified	Uncertain significance (Nov 09, 2021)
1-62210440-G-C		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
L1TD1	protein_coding	protein_coding	ENST00000498273	2	17498

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.33e-7	0.428	122744	11	1981	124736	0.00802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.887	448	398	1.13	0.0000179	5742
Missense in Polyphen		68	69.27	0.98167		1144
Synonymous	-3.13	191	143	1.33	0.00000677	1529
Loss of Function	0.676	11	13.7	0.803	6.67e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00882	0.00881
Ashkenazi Jewish	0.0182	0.0181
East Asian	0.00	0.00
Finnish	0.00380	0.00366
European (Non-Finnish)	0.0115	0.0115
Middle Eastern	0.00	0.00
South Asian	0.00376	0.00371
Other	0.0112	0.0112

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0716

Intolerance Scores

• loftool: 0.964
• rvis_EVS: 1.94
• rvis_percentile_EVS: 97.51

Haploinsufficiency Scores

• pHI: 0.319
• hipred: N
• hipred_score: 0.123
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0649

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: L1td1
• Phenotype: normal phenotype

Gene ontology

• Biological process: transposition, RNA-mediated
• Cellular component: ribonucleoprotein complex
• Molecular function: single-stranded RNA binding