Gene Gene information from NCBI Gene database.
Entrez ID 4913
Gene name Nth like DNA glycosylase 1
Gene symbol NTHL1
Synonyms (NCBI Gene)
FAP3NTH1OCTS3hNTH1
Chromosome 16
Chromosome location 16p13.3
Summary 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/apyrimid
SNPs SNP information provided by dbSNP.
16
SNP ID Visualize variation Clinical significance Consequence
rs146347092 G>A Conflicting-interpretations-of-pathogenicity, uncertain-significance Coding sequence variant, stop gained
rs369076851 G>A Likely-benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
rs371328106 G>A,C,T Likely-benign, pathogenic Stop gained, coding sequence variant, intron variant, synonymous variant
rs372946560 C>T Pathogenic Splice donor variant
rs374489979 G>A,T Pathogenic Intron variant, synonymous variant, coding sequence variant, stop gained
miRNA miRNA information provided by mirtarbase database.
15
miRTarBase ID miRNA Experiments Reference
MIRT022743 hsa-miR-124-3p Proteomics 18668037
MIRT031740 hsa-miR-16-5p Proteomics 18668040
MIRT049546 hsa-miR-92a-3p CLASH 23622248
MIRT048860 hsa-miR-93-5p CLASH 23622248
MIRT1196056 hsa-miR-421 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
39
GO ID Ontology Definition Evidence Reference
GO:0000703 Function Oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity IBA
GO:0000703 Function Oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity IEA
GO:0000703 Function Oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity TAS
GO:0003677 Function DNA binding IEA
GO:0003684 Function Damaged DNA binding IDA 9927729
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602656 8028 ENSG00000065057
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P78549
Protein name Endonuclease III-like protein 1 (hNTH1) (EC 3.2.2.-) (EC 4.2.99.18) (Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase) (DNA glycosylase/AP lyase)
Protein function Bifunctional DNA N-glycosylase with associated apurinic/apyrimidinic (AP) lyase function that catalyzes the first step in base excision repair (BER), the primary repair pathway for the repair of oxidative DNA damage (PubMed:29610152, PubMed:9927
PDB 7RDS , 7RDT
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00730 HhH-GPD 134 272 HhH-GPD superfamily base excision DNA repair protein Domain
PF00633 HHH 199 228 Helix-hairpin-helix motif Motif
Tissue specificity TISSUE SPECIFICITY: Widely expressed with highest levels in heart and lowest levels in lung and liver. {ECO:0000269|PubMed:8990169, ECO:0000269|PubMed:9831664}.
Sequence
MCSPQESGMTALSARMLTRSRSLGPGAGPRGCREEPGPLRRREAAAEARKSHSPVKRPRK
AQRLRVAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIRAMRNKKDAPVDHLGTEHCYD
SSAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGLTVDSILQTDDATLGKLIYPVG
FWRSKVKYIKQTSAILQQ
HYGGDIPASVAELVALPGVGPKMAHLAMAVAWGTVSGIAVDT
HVHRIANRLRWTKKATKSPEETRAALEEWLPR
ELWHEINGLLVGFGQQTCLPVHPRCHAC
LNQALCPAAQGL
Sequence length 312
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Base excision repair   Recognition and association of DNA glycosylase with site containing an affected pyrimidine
Cleavage of the damaged pyrimidine
Displacement of DNA glycosylase by APEX1
Defective NTHL1 substrate processing
Defective NTHL1 substrate binding
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
18
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Familial adenomatous polyposis 1 Likely pathogenic rs2548315238 RCV004720390
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial adenomatous polyposis 3 Pathogenic; Likely pathogenic rs879181418, rs1567369975, rs2150945390, rs2150945928, rs2150947238, rs2150957715, rs2150938327, rs2150942179, rs1455020789, rs1567369247, rs2150942398, rs2084372140, rs2150938411, rs2150941243, rs779757251
View all (69 more)
RCV003316841
RCV003458225
RCV005423985
RCV003458226
RCV003458228
View all (83 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hereditary cancer-predisposing syndrome Pathogenic; Likely pathogenic rs879181418, rs1567369975, rs2150945390, rs2150945928, rs2150947238, rs2150957715, rs2150942179, rs2084241184, rs1567369247, rs2150942398, rs2084372140, rs2150938411, rs2150946400, rs2150946310, rs2150946263
View all (46 more)
RCV005453291
RCV004639609
RCV003169950
RCV002438888
RCV003298633
View all (58 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NTHL1-deficiency tumor predisposition syndrome Likely pathogenic; Pathogenic rs745671590 RCV005367487
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CANCER GenCC
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
FOCAL CORTICAL DYSPLASIA OF TAYLOR Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Glioma susceptibility 1 Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma of duodenum Adenocarcinoma Of Duodenum HPO_DG
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of large intestine Colorectal Cancer CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of pancreas Pancreatic adenocarcinoma HPO_DG
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 31285513
★☆☆☆☆
Found in Text Mining only
Adenoma of large intestine Colorectal adenoma BEFREE 18515411, 23951112, 31227763
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 25938944, 28331556, 29105096, 29702101, 30753826, 30904095
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome CTD_human_DG 25938944
★☆☆☆☆
Found in Text Mining only
Attenuated familial adenomatous polyposis Adenomatous polyposis Pubtator 31227763, 31285513 Associate
★☆☆☆☆
Found in Text Mining only
Bladder Neoplasm Bladder Neoplasm HPO_DG
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma HPO_DG
★☆☆☆☆
Found in Text Mining only