L1TD1

protein-coding

LINE1 type transposase domain containing 1

Gene summary

Predicted to enable sequence-specific mRNA binding activity and single-stranded RNA binding activity. Predicted to be involved in 3'-UTR-mediated mRNA stabilization and retrotransposition. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_019079.5

Inheritance

—

ClinVar variants

U:77B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr1:62,194,790-62,235,060

External References & Databases

Ensembl (ENSG00000240563)

Transcript & Mutation Effects

hg38 • Region Span ~40.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to L1TD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019079.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			77 clinvar	4 clinvar		81
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	5	1	83

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019079.5	RefSeq	NP_061952.3	2	MANE Select
ENST00000498273.2	Ensembl	ENSP00000419901.1	2	MANE Select
NM_001164835.2	RefSeq	NP_001158307.1	2	Standard
ENST00000928897.1	Ensembl	ENSP00000598956.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transposition, RNA-mediated

Molecular Function

single-stranded RNA binding

Cellular Component

ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000498273
Coding exons: 2
Length: 17498
Individuals with no LoFs: 122744
Homozygous LoFs: 11
Heterozygous LoFs: 1981
Defined: 124736
p: 0.00802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.887	448	398	1.13	0.0000179	5742
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0019	0.0019	notable
Latino/Admixed American	0.0069	0.0068	notable
Ashkenazi Jewish	0.018	0.018	notable
East Asian	0	0.0	absent
Finnish	0.0038	0.0037	notable
European (Non-Finnish)	0.012	0.012	notable
South Asian	0.0038	0.0037	notable
Other	0.011	0.011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0716

Intolerance Scores

LoFtool: 0.964
RVIS EVS: 1.94
RVIS percentile EVS: 97.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0649

Gene Damage Prediction

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