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Gene

NTHL1

nth like DNA glycosylase 1

Summary

Cytogenetic location
16p13.3
Coordinates
Chromosome 16: 2,039,820–2,047,834 (GRCh38)
Exons
6 exons across 8 kb
Protein
304 amino acids
Inheritance
Autosomal dominant
Also known as
NTH1, OCTS3
MANE Select transcript
ENST00000651570.2NM_002528.7
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Colorectal Cancer & Polyposis

    • Familial adenomatous polyposis (classic or attenuated)Autosomal dominant

      Hundreds to thousands of colorectal adenomas with a near-certain risk of colorectal cancer without treatment; includes APC-related FAP and MUTYH-, NTHL1- and MSH3-related polyposis.

      • 3 GenCC submitters rate it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How NTHL1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where NTHL1 sits. NTHL1 and 51 genes near it on chromosome 16, from 1,543,827 to 2,543,826.Chromosome 1616p13.3p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.31.6 Mb1.8 Mb2 Mb2.2 Mb2.4 MbIFT140: 1,510,427–1,612,082, reverse strandIFT140TMEM204: 1,528,674–1,555,580, forward strandTMEM204CRAMP1: 1,612,337–1,677,908, forward strandCRAMP1: 1,632,259–1,686,715, forward strandJPT2: 1,678,256–1,702,859, forward strandJPT2MAPK8IP3: 1,706,166–1,770,374, forward strandNME3: 1,770,317–1,771,746, reverse strandMRPS34: 1,771,889–1,773,487, reverse strandEME2: 1,772,283–1,781,708, forward strandSPSB3: 1,776,710–1,793,700, reverse strandNUBP2: 1,782,932–1,789,189, forward strandNUBP2IGFALS: 1,790,227–1,794,971, reverse strandIGFALSHAGH: 1,795,620–1,827,187, reverse strandHAGHFAHD1: 1,826,967–1,842,053, forward strandFAHD1MEIOB: 1,833,986–1,884,294, reverse strandMEIOBHS3ST6: 1,911,475–1,918,415, reverse strandHS3ST6MSRB1: 1,935,685–1,943,270, reverse strandMSRB1RPL3L: 1,943,791–1,957,606, reverse strandNDUFB10: 1,959,500–1,962,105, forward strandRPS2: 1,961,987–1,965,510, reverse strandRPS2RNF151: 1,966,823–1,968,975, forward strandTBL3: 1,971,972–1,983,056, forward strandNOXO1: 1,978,912–1,984,636, reverse strandGFER: 1,983,699–1,987,749, forward strandSYNGR3: 1,989,637–1,994,275, forward strandZNF598: 1,997,654–2,009,821, reverse strandZNF598NPW: 2,009,926–2,020,755, forward strandNPWNHERF2: 2,025,356–2,039,026, forward strandNHERF2NTHL1: 2,039,820–2,047,834, reverse strandNTHL1TSC2: 2,047,345–2,089,491, forward strandTSC2PKD1: 2,088,708–2,135,898, reverse strandPKD1RAB26: 2,140,803–2,154,165, forward strandRAB26TRAF7: 2,155,692–2,178,129, forward strandTRAF7CASKIN1: 2,177,180–2,196,788, reverse strandCASKIN1MLST8: 2,204,248–2,209,453, forward strandMLST8BRICD5: 2,209,252–2,210,905, reverse strandBRICD5PGP: 2,211,593–2,214,846, reverse strandPGPE4F1: 2,223,440–2,235,743, forward strandDNASE1L2: 2,235,816–2,238,711, forward strandECI1: 2,239,376–2,252,300, reverse strandRNPS1: 2,253,116–2,268,413, reverse strandRNPS1ABCA3: 2,275,878–2,340,788, reverse strandABCA3CCNF: 2,429,394–2,458,913, forward strandCCNFTEDC2: 2,460,085–2,464,963, forward strandTEDC2NTN3: 2,471,286–2,474,145, forward strandNTN3TBC1D24: 2,475,051–2,509,671, forward strandTBC1D24: 2,496,032–2,520,218, forward strandATP6V0C: 2,513,713–2,520,218, forward strand: 2,513,965–2,527,955, forward strandAMDHD2: 2,520,340–2,531,422, forward strandCEMP1: 2,530,035–2,531,417, reverse strandPDPK1: 2,537,969–2,603,190, forward strandDiagram of NTHL1: 6 exons on the reverse strand of chromosome 16Exon 6: 8 known disease-causing sitesExon 5: 14 known disease-causing sitesExon 4: 19 known disease-causing sitesExon 3: 24 known disease-causing sitesExon 2: 30 known disease-causing sitesExon 1: 12 known disease-causing sitesExon 6: 2,039,820–2,040,047, 228 basesExon 5: 2,040,133–2,040,238, 106 basesExon 4: 2,043,567–2,043,726, 160 basesExon 3: 2,044,630–2,044,800, 171 basesExon 2: 2,046,128–2,046,366, 239 basesExon 1: 2,047,709–2,047,834, 126 bases6543215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1 kb of the gene's 8 kb; 915 of those bases code for the protein.

How a genome test reads NTHL1

121

positions in NTHL1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 8 kb of NTHL1, introns included, not only the 1 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). NTHL1 gene: nth like DNA glycosylase 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/nthl1

Vancouver

Dante Labs. NTHL1 gene: nth like DNA glycosylase 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/nthl1

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