NTHL1

Chr 16

nth like DNA glycosylase 1

Also known as: FAP3, NTH1, OCTS3, hNTH1

NCBI Gene: 4913ENSG00000065057UniProt: P78549

The protein encoded by this gene is a DNA N-glycosylase of the endonuclease III family. Like a similar protein in E. coli, the encoded protein has DNA glycosylase activity on DNA substrates containing oxidized pyrimidine residues and has apurinic/apyrimidinic lyase activity. [provided by RefSeq, Oct 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtFamilial adenomatous polyposis 3

Clinical highlights

Gene-disease validity (ClinGen)
NTHL1-deficiency tumor predisposition syndrome · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
26
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
1.59
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — NTHL1
Authoritative clinical overview · Recommended first read
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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?
1.59LOEUF
pLI 0.000
Z-score -0.10
OE 1.03 (0.68–1.59)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
-0.80Z-score
OE missense 1.16 (1.04–1.29)
233 obs / 201.2 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?1.03 (0.68–1.59)
0≤0.351.4
Missense OE?1.16 (1.04–1.29)
0≤0.61.4
Synonymous OE?0.94
0≤1.21.6
LoF obs/exp: 14 / 13.6Missense obs/exp: 233 / 201.2Syn Z: 0.41

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

NTHL1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients