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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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

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

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

1364

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Familial adenomatous polyposis 1	Likely pathogenic	rs2548315238	RCV004720390
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 RCV003458227 RCV001533141 RCV003470889 RCV003458237 RCV004591684 RCV004043465 RCV003458236 RCV003458240 RCV003458241 RCV003458232 RCV003458244 RCV003458245 RCV003459748 RCV004572802 RCV003458247 RCV003458248 RCV003458250 RCV000202319 RCV003336800 RCV003140374 RCV003140385 RCV003471614 RCV003471617 RCV003471618 RCV003463213 RCV003471619 RCV003458299 RCV003458300 RCV003458301 RCV003458302 RCV003458303 RCV003458304 RCV003458305 RCV003458306 RCV003458307 RCV003458308 RCV003458309 RCV003458310 RCV003458311 RCV003458313 RCV003458314 RCV003458315 RCV003458316 RCV003458317 RCV003458318 RCV003458319 RCV003458320 RCV004786971 RCV005871277 RCV004374039 RCV004442559 RCV004442569 RCV004442595 RCV004589195 RCV004589254 RCV004589333 RCV003458205 RCV001310141 RCV003458204 RCV001535451 RCV001784408 RCV003458215 RCV003458214 RCV003458211 RCV003458209 RCV003458212 RCV003458218 RCV003458208 RCV003458206 RCV003458207 RCV003458216 RCV004789209 RCV003458217 RCV002290473 RCV003458210 RCV003458213 RCV000989411 RCV003458220 RCV003336244 RCV003458221 RCV003469263 RCV005621084 RCV003458312
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 RCV004037691 RCV003355542 RCV005374964 RCV004945862 RCV004043464 RCV002441011 RCV002386918 RCV002257312 RCV002255965 RCV002255966 RCV002258606 RCV002333817 RCV002375781 RCV002328735 RCV002378578 RCV002401252 RCV005377278 RCV003167845 RCV004946124 RCV003352802 RCV003164928 RCV003293266 RCV003293268 RCV004654225 RCV005455797 RCV004654226 RCV004943041 RCV005387177 RCV004516067 RCV004516061 RCV002424557 RCV002256456 RCV004026006 RCV001018044 RCV001027136 RCV002363103 RCV001023343 RCV002332650 RCV002336609 RCV002332652 RCV002332722 RCV002352346 RCV001021416 RCV002352342 RCV002363139 RCV003362964 RCV004029040 RCV001024197 RCV001011341 RCV001011335 RCV001022918 RCV001021039 RCV001015982 RCV002411615 RCV002258127 RCV005372594 RCV002393598 RCV004636743
NTHL1-deficiency tumor predisposition syndrome	Likely pathogenic; Pathogenic	rs745671590	RCV005367487
NTHL1-related disorder	Likely pathogenic; Pathogenic	rs146347092	RCV004751695

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Uncertain significance	rs750992242	RCV005910979
Glioma susceptibility 1	Uncertain significance	rs748576083	RCV005901970
Inherited polyposis and early onset colorectal cancer - germline testing	Conflicting classifications of pathogenicity	rs1805378	RCV005430822
Lung cancer	Uncertain significance; Benign; Likely benign	rs772690647, rs3211970	RCV005925680 RCV005903727
Malignant tumor of esophagus	Benign; Likely benign	rs3211970	RCV005903726
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs529341502	RCV005902014
Pancreatic adenocarcinoma	Uncertain significance	rs748576083	RCV005901971
Thymoma	Likely benign	rs767225352	RCV005912711
Uterine corpus endometrial carcinoma	Conflicting classifications of pathogenicity; Uncertain significance	rs529341502, rs2084244745	RCV005902015 RCV005909008

Show/Hide Text Mining Associations (28)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)