NEIL1

nei like DNA glycosylase 1, the group of DNA glycosylases

Basic information

Region (hg38): 15:75346954-75357115

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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			18	4	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				1		1
non coding		1	18	4	5	28
Total	0	1	36	12	7

Variants in NEIL1

This is a list of pathogenic ClinVar variants found in the NEIL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-75347736-G-A			Benign (Jan 16, 2020)
15-75347788-G-A			Likely benign (Apr 15, 2020)
15-75348082-C-T			Benign (Aug 20, 2019)
15-75348228-A-G			Benign (Nov 12, 2018)
15-75348245-C-T			Likely benign (Oct 29, 2020)
15-75349051-C-G			Benign/Likely benign (Mar 17, 2021)
15-75349059-C-G		not specified	Uncertain significance (Aug 12, 2022)
15-75349108-C-A			Benign (Oct 18, 2018)
15-75349115-G-C		not specified	Uncertain significance (Aug 02, 2023)
15-75349179-G-A		not specified	Uncertain significance (Mar 16, 2022)
15-75349179-G-C		not specified	Uncertain significance (Jun 27, 2022)
15-75349180-A-T		not specified	Uncertain significance (Jun 27, 2022)
15-75349215-G-GC			Conflicting classifications of pathogenicity (Dec 31, 2019)
15-75349218-C-T		not specified	Uncertain significance (Nov 29, 2023)
15-75349261-G-A		not specified	Uncertain significance (Apr 24, 2024)
15-75349269-C-T		not specified	Uncertain significance (May 02, 2024)
15-75349341-T-C			Benign/Likely benign (Apr 01, 2023)
15-75349373-G-A			Likely benign (Apr 15, 2020)
15-75351274-C-CTT		NEIL1-related disorder	Benign (Oct 28, 2019)
15-75352125-G-A		not specified	Uncertain significance (May 25, 2022)
15-75352222-C-G			Benign (Jul 31, 2018)
15-75352229-C-T		not specified	Uncertain significance (Feb 02, 2022)
15-75352349-G-A		not specified	Uncertain significance (Oct 19, 2021)
15-75352579-T-TCCTGCC		NEIL1-related disorder	Likely benign (May 30, 2019)
15-75352671-C-T		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEIL1	protein_coding	protein_coding	ENST00000564784	9	8297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.96e-7	0.859	123446	18	2284	125748	0.00920

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.259	259	248	1.05	0.0000161	2461
Missense in Polyphen		87	85.14	1.0218		870
Synonymous	-1.56	120	100	1.20	0.00000570	824
Loss of Function	1.53	13	20.5	0.635	0.00000114	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00960	0.00949
Ashkenazi Jewish	0.00837	0.00817
East Asian	0.000494	0.000489
Finnish	0.00679	0.00579
European (Non-Finnish)	0.0158	0.0147
Middle Eastern	0.000494	0.000489
South Asian	0.00189	0.00183
Other	0.0133	0.0126

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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