ASTE1

Chr 3

asteroid structure-specific endonuclease 1

Also known as: HT001

NCBI Gene: 28990 ENSG00000034533 UniProt: Q2TB18 OMIM: 620693

Enables 3' overhang single-stranded DNA endonuclease activity. Involved in double-strand break repair via homologous recombination and double-strand break repair via nonhomologous end joining. Implicated in Lynch syndrome and mismatch repair cancer syndrome. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.14

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.14LOEUF

pLI 0.000

Z-score 1.06

OE 0.76 (0.52–1.14)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.86Z-score

OE missense 0.87 (0.80–0.96)

316 obs / 362.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.76 (0.52–1.14)

0≤0.351.4

Missense OE?0.87 (0.80–0.96)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 17 / 22.4Missense obs/exp: 316 / 362.2Syn Z: -0.05

Background carrier burden — how many people carry a rare variant somewhere in ASTE1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 70

795 rare PASS variants

Rare truncating (LoF)

1 in 550

159 rare PASS variants

Rare synonymous (reference)

1 in 190

320 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ASTE1. 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 110	1 in 560
South Asian	~43k	1 in 66	1 in 760
Remaining (unassigned)	~30k	1 in 67	1 in 1,000
European (Finnish)	~27k	1 in 240	1 in 1,300
Admixed American	~22k	1 in 75	1 in 230
African / African American	~21k	1 in 57	1 in 640
East Asian	~20k	1 in 73	1 in 640
Ashkenazi Jewish	~13k	1 in 450	≈ 1 in 3,200
Middle Eastern	~2,884	1 in 55	1 in 470

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 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓