XNDC1N

Chr 11

XRCC1 N-terminal domain containing 1, N-terminal like

NCBI Gene: 100133315 ENSG00000254469 UniProt: Q6ZNB5

Predicted to enable damaged DNA binding activity. Predicted to be involved in single strand break repair. Located in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

Research

Predicted to enable damaged DNA binding activity. Predicted to be involved in single strand break repair. Located in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.77

LOEUF

—

Mechanism

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.77LOEUF

pLI 0.000

Z-score -0.36

OE 1.12 (0.70–1.77)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.21Z-score

OE missense 0.68 (0.57–0.82)

79 obs / 115.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.12 (0.70–1.77)

0≤0.351.4

Missense OE?0.68 (0.57–0.82)

0≤0.61.4

Synonymous OE?0.71

0≤1.21.6

LoF obs/exp: 11 / 9.8Missense obs/exp: 79 / 115.7Syn Z: 1.54

Background carrier burden — how many people carry a rare variant somewhere in XNDC1N?

gnomAD v4 · ~729k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 95

381 rare PASS variants

Rare truncating (LoF)

1 in 140

77 rare PASS variants

Rare synonymous (reference)

1 in 310

133 rare PASS variants

Rare missense and truncating variants are carried at similar rates in XNDC1N; this gene does not show strong loss-of-function constraint by this measure. 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 190	1 in 650
South Asian	~43k	1 in 140	1 in 700
Remaining (unassigned)	~30k	1 in 76	1 in 400
European (Finnish)	~27k	1 in 330	1 in 1,800
Admixed American	~22k	1 in 87	1 in 220
African / African American	~21k	1 in 120	1 in 190
East Asian	~20k	1 in 170	1 in 400
Ashkenazi Jewish	~13k	1 in 930	≈ 1 in 10,000
Middle Eastern	~2,066	1 in 130	≈ 1 in 2,000

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): 1 of 5 coding exons well covered in gnomAD exomes; exons 2, 3, 4, 5 poorly covered. Genomes: all 5.? see exons ↓