EXD1

Chr 15

exonuclease 3'-5' domain containing 1

Also known as: EXDL1

NCBI Gene: 161829 ENSG00000178997 UniProt: Q8NHP7 OMIM: 621709

Predicted to enable RNA binding activity and protein homodimerization activity. Predicted to be involved in piRNA processing. Predicted to be located in P granule. Predicted to be part of PET complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.26

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.26LOEUF

pLI 0.000

Z-score 0.53

OE 0.88 (0.63–1.26)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.11Z-score

OE missense 1.02 (0.92–1.13)

267 obs / 261.9 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.88 (0.63–1.26)

0≤0.351.4

Missense OE?1.02 (0.92–1.13)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 22 / 24.9Missense obs/exp: 267 / 261.9Syn Z: -0.08

Background carrier burden — how many people carry a rare variant somewhere in EXD1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 76

818 rare PASS variants

Rare truncating (LoF)

1 in 700

169 rare PASS variants

Rare synonymous (reference)

1 in 360

259 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for EXD1. 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 92	1 in 780
South Asian	~43k	1 in 85	1 in 380
Remaining (unassigned)	~30k	1 in 68	1 in 490
European (Finnish)	~27k	1 in 240	1 in 470
Admixed American	~22k	1 in 81	1 in 780
African / African American	~21k	1 in 71	1 in 550
East Asian	~20k	1 in 71	1 in 520
Ashkenazi Jewish	~13k	1 in 290	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 69	≈ 1 in 2,900

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.