L1TD1

Chr 1

LINE1 type transposase domain containing 1

Also known as: ECAT11

NCBI Gene: 54596 ENSG00000240563 UniProt: Q5T7N2 OMIM: 621222

The protein is predicted to bind single-stranded RNA and be involved in retrotransposition. The gene shows no constraint against loss-of-function variants (pLI near 0, LOEUF 1.3), and no established human disease associations have been reported for L1TD1 mutations.

OMIM ResearchSummary from RefSeq

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]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.33

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.33LOEUF

pLI 0.000

Z-score 0.68

OE 0.80 (0.50–1.33)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.89Z-score

OE missense 1.13 (1.04–1.22)

448 obs / 398.2 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.80 (0.50–1.33)

0≤0.351.4

Missense OE?1.13 (1.04–1.22)

0≤0.61.4

Synonymous OE?1.33

0≤1.21.6

LoF obs/exp: 11 / 13.7Missense obs/exp: 448 / 398.2Syn Z: -3.13

Background carrier burden — how many people carry a rare variant somewhere in L1TD1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 46

1,227 rare PASS variants

Rare truncating (LoF)

1 in 290

283 rare PASS variants

Rare synonymous (reference)

1 in 70

456 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for L1TD1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 62	1 in 350
South Asian	~43k	1 in 44	1 in 150
Remaining (unassigned)	~30k	1 in 46	1 in 240
European (Finnish)	~27k	1 in 140	1 in 320
Admixed American	~22k	1 in 44	1 in 180
African / African American	~21k	1 in 41	1 in 190
East Asian	~20k	1 in 58	1 in 180
Ashkenazi Jewish	~13k	1 in 180	≈ 1 in 4,200
Middle Eastern	~2,884	1 in 72	1 in 290

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓