GeneBe

NEIL1

nei like DNA glycosylase 1, the group of DNA glycosylases

Basic information

Region (hg38): 15:75346955-75357115

Links

ENSG00000140398 ∙ NCBI:79661 ∙ OMIM:608844 ∙ HGNC:18448 ∙ Uniprot:Q96FI4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEIL1 gene.

  • not_specified (47 variants)
  • not_provided (10 variants)
  • NEIL1-related_disorder (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEIL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024608.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
 3
missense
45
clinvar
6
clinvar
2
clinvar
 53
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 0 0 45 11 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NEIL1protein_codingprotein_codingENST00000564784 98297
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
4.96e-70.8591234461822841257480.00920
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2592592481.050.00001612461
Missense in Polyphen8785.141.0218870
Synonymous-1.561201001.200.00000570824
Loss of Function1.531320.50.6350.00000114206

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.009600.00949
Ashkenazi Jewish0.008370.00817
East Asian0.0004940.000489
Finnish0.006790.00579
European (Non-Finnish)0.01580.0147
Middle Eastern0.0004940.000489
South Asian0.001890.00183
Other0.01330.0126

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, formamidopyrimidine (Fapy) and 5-hydroxyuracil. Has marginal activity towards 8- oxoguanine. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Has DNA glycosylase/lyase activity towards mismatched uracil and thymine, in particular in U:C and T:C mismatches. Specifically binds 5- hydroxymethylcytosine (5hmC), suggesting that it acts as a specific reader of 5hmC. {ECO:0000269|PubMed:11904416, ECO:0000269|PubMed:12200441, ECO:0000269|PubMed:12509226, ECO:0000269|PubMed:14522990}.;
Pathway
Base excision repair - Homo sapiens (human);DNA Repair;Recognition and association of DNA glycosylase with site containing an affected pyrimidine;Cleavage of the damaged pyrimidine ;Depyrimidination;Base-Excision Repair, AP Site Formation;Resolution of Abasic Sites (AP sites);Base Excision Repair;APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway (Consensus)

Recessive Scores

pRec
0.184

Intolerance Scores

loftool
0.862
rvis_EVS
0.8
rvis_percentile_EVS
87.54

Haploinsufficiency Scores

pHI
0.142
hipred
N
hipred_score
0.423
ghis
0.526

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.910

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Neil1
Phenotype
adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; neoplasm; reproductive system phenotype; liver/biliary system phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype;

Gene ontology

Biological process
base-excision repair;nucleotide-excision repair;response to oxidative stress;negative regulation of nuclease activity;depyrimidination
Cellular component
nucleus;nucleoplasm;chromosome;cytoplasm;microtubule organizing center
Molecular function
damaged DNA binding;DNA-(apurinic or apyrimidinic site) endonuclease activity;protein C-terminus binding;zinc ion binding;hydrolase activity, acting on glycosyl bonds;DNA N-glycosylase activity;class I DNA-(apurinic or apyrimidinic site) endonuclease activity