Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	4913
Gene name Gene Name - the full gene name approved by the HGNC.	Nth like DNA glycosylase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NTHL1
Synonyms (NCBI Gene) Gene synonyms aliases	FAP3, NTH1, OCTS3, hNTH1
Chromosome Chromosome number	16
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	16p13.3
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(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
rs753029097	C>T	Uncertain-significance, likely-pathogenic	Stop gained, coding sequence variant
rs758667255	G>A	Pathogenic	Coding sequence variant, stop gained, intron variant
rs759955745	->GTAC	Pathogenic	Frameshift variant, coding sequence variant, intron variant
rs779757251	C>T	Likely-pathogenic	Splice acceptor variant
rs919177150	C>A,T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, stop gained
rs1173366565	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1198246754	G>A	Pathogenic	Coding sequence variant, intron variant, stop gained
rs1596220242	C>T	Likely-pathogenic	Intron variant, splice donor variant
rs1596220332	C>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1596220365	->G	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1596220478	AG>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant

Show/Hide all(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
MIRT1196057	hsa-miR-4272	CLIP-seq
MIRT1196058	hsa-miR-4709-5p	CLIP-seq
MIRT2056882	hsa-miR-27a	CLIP-seq
MIRT2056883	hsa-miR-27b	CLIP-seq
MIRT2056884	hsa-miR-513a-5p	CLIP-seq
MIRT2056882	hsa-miR-27a	CLIP-seq
MIRT2056883	hsa-miR-27b	CLIP-seq
MIRT2285350	hsa-miR-4701-5p	CLIP-seq
MIRT2056884	hsa-miR-513a-5p	CLIP-seq
MIRT2285351	hsa-miR-588	CLIP-seq

Show/Hide all(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
GO:0003690	Function	Double-stranded DNA binding	IDA	15358233
GO:0003824	Function	Catalytic activity	IEA
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	IBA
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	IDA	8990169, 9927729
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	IEA
GO:0004519	Function	Endonuclease activity	TAS	9831664
GO:0005515	Function	Protein binding	IPI	9927729, 15358233
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	12531031
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IEA
GO:0006281	Process	DNA repair	IEA
GO:0006284	Process	Base-excision repair	IEA
GO:0006285	Process	Base-excision repair, AP site formation	IBA
GO:0006285	Process	Base-excision repair, AP site formation	IDA	9927729, 15358233
GO:0006285	Process	Base-excision repair, AP site formation	IEA
GO:0006289	Process	Nucleotide-excision repair	IBA
GO:0006289	Process	Nucleotide-excision repair	IDA	8990169
GO:0006289	Process	Nucleotide-excision repair	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0008534	Function	Oxidized purine nucleobase lesion DNA N-glycosylase activity	TAS
GO:0016787	Function	Hydrolase activity	IEA
GO:0016798	Function	Hydrolase activity, acting on glycosyl bonds	IEA
GO:0016829	Function	Lyase activity	IEA
GO:0019104	Function	DNA N-glycosylase activity	IDA	10882850
GO:0019104	Function	DNA N-glycosylase activity	IEA
GO:0045008	Process	Depyrimidination	TAS
GO:0046872	Function	Metal ion binding	IEA
GO:0051536	Function	Iron-sulfur cluster binding	IEA
GO:0051539	Function	4 iron, 4 sulfur cluster binding	IEA
GO:0140078	Function	Class I DNA-(apurinic or apyrimidinic site) endonuclease activity	IDA	8990169
GO:0140078	Function	Class I DNA-(apurinic or apyrimidinic site) endonuclease activity	IEA

MIM	HGNC	e!Ensembl
602656	8028	ENSG00000065057

Protein

UniProt ID

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
FWRSKVKYIKQTSAILQQHYGGDIPASVAELVALPGVGPKMAHLAMAVAWGTVSGIAVDT
HVHRIANRLRWTKKATKSPEETRAALEEWLPRELWHEINGLLVGFGQQTCLPVHPRCHAC
LNQALCPAAQGL

Sequence length

312

Interactions

View interactions

	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

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Adenomatous Polyposis	familial adenomatous polyposis 3	rs919177150, rs779757251, rs1198246754, rs1239874051, rs1596220332, rs1411394625, rs374489979, rs749908882, rs758667255, rs1314290585, rs372946560, rs1596220478, rs1290880136, rs1173366565, rs371328106 View all (9 more)	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Breast Cancer	breast cancer	N/A	N/A	GenCC
Meningioma	meningioma	N/A	N/A	GenCC
TUMOR PREDISPOSITION SYNDROME	NTHL1-deficiency tumor predisposition syndrome	N/A	N/A	GenCC

Show/Hide Text Mining Associations (28)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenoma	Associate	23951112
Adenomatous Polyposis Coli	Associate	30753826, 31227763, 33664379, 39519399
Attenuated familial adenomatous polyposis	Associate	31227763, 31285513
Breast Neoplasms	Associate	28912133, 30753826, 34250384, 38036545
Carcinoma Non Small Cell Lung	Associate	38384388
Colorectal Neoplasms	Associate	17029639, 28445943, 30267214, 30753826, 31227763, 32949222, 37834005, 38036545
Colorectal Neoplasms Hereditary Nonpolyposis	Associate	31227763
Drug Related Side Effects and Adverse Reactions	Associate	18307537
Gastrointestinal Diseases	Associate	37402954
Genetic Diseases Inborn	Associate	37402954
Hepatoblastoma	Associate	37834005
Intestinal Neoplasms	Associate	37834005
Intestinal Polyposis	Associate	29367705, 34250384, 37834005
Kidney Diseases	Associate	36581342
Kidney Neoplasms	Associate	36581342
Meningioma	Associate	31227763
Neoplasms	Stimulate	21187477
Neoplasms	Associate	23940330, 28912133, 29522130, 30753826, 32109332, 34250384, 37834005, 38036545, 38384388
Neoplasms	Inhibit	36581342
Neurilemmoma	Associate	37402954
Neuroectodermal Tumors Primitive	Associate	29092957
Neuroendocrine Tumors	Associate	29092957
Polycystic Kidney Autosomal Dominant	Associate	36581342
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	37402954
Prostate Cancer Hereditary 8	Associate	31227763
Tuberous Sclerosis	Associate	36581342
Uveal melanoma	Associate	37402954
Vagus Nerve Diseases	Associate	37834005

NTHL1 (nth like DNA glycosylase 1)