NEIL2

nei like DNA glycosylase 2, the group of DNA glycosylases

Basic information

Region (hg38): 8:11769638-11787345

Links

ENSG00000154328 ∙ NCBI:252969 ∙ OMIM:608933 ∙ HGNC:18956 ∙ Uniprot:Q969S2 ∙ 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 NEIL2 gene.

• Inborn genetic diseases (19 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEIL2 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				2	3	5
missense			18	2	2	22
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	19	4	6

Variants in NEIL2

This is a list of pathogenic ClinVar variants found in the NEIL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-11771462-G-A			Likely benign (Apr 01, 2022)
8-11771508-C-G		not specified	Uncertain significance (Feb 06, 2023)
8-11771524-G-C		High myopia	Uncertain significance (Dec 17, 2018)
8-11771550-G-A		not specified	Uncertain significance (Jun 29, 2022)
8-11771561-G-A			Benign (Apr 05, 2018)
8-11771576-G-C		not specified	Uncertain significance (Apr 10, 2023)
8-11771581-C-G		not specified	Uncertain significance (Jun 24, 2022)
8-11779664-C-G			Likely benign (Apr 05, 2018)
8-11779680-C-T		not specified	Likely benign (May 08, 2023)
8-11779766-C-T			Benign (Jun 06, 2018)
8-11779785-C-T		not specified	Uncertain significance (Dec 27, 2023)
8-11779796-G-T		not specified	Uncertain significance (Jan 30, 2024)
8-11779827-C-T		not specified	Uncertain significance (Jan 09, 2024)
8-11779843-GA-G			Uncertain significance (Jan 14, 2016)
8-11779849-G-T		not specified	Uncertain significance (Dec 09, 2023)
8-11779856-G-C		not specified	Uncertain significance (Oct 10, 2023)
8-11779879-C-T			Likely benign (Mar 30, 2018)
8-11779911-A-C		not specified	Uncertain significance (Jun 24, 2022)
8-11779911-A-T		not specified	Uncertain significance (Aug 04, 2023)
8-11779914-C-T		not specified	Uncertain significance (Mar 01, 2024)
8-11779921-G-T		not specified	Uncertain significance (Dec 19, 2023)
8-11779934-A-G		not specified	Uncertain significance (Jan 05, 2022)
8-11783220-G-A		not specified	Uncertain significance (Dec 30, 2023)
8-11783229-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-11783277-T-A		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEIL2	protein_coding	protein_coding	ENST00000284503	4	17708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.87e-11	0.0224	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.09	264	184	1.43	0.0000100	2155
Missense in Polyphen		88	62.001	1.4193		828
Synonymous	-2.84	112	79.7	1.40	0.00000488	653
Loss of Function	-0.530	15	12.9	1.16	6.23e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000821	0.000821
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000310	0.000308
Middle Eastern	0.000272	0.000272
South Asian	0.00111	0.00111
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Has DNA glycosylase activity towards 5-hydroxyuracil and other oxidized derivatives of cytosine with a preference for mismatched double-stranded DNA (DNA bubbles). Has low or no DNA glycosylase activity towards thymine glycol, 2-hydroxyadenine, hypoxanthine and 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. {ECO:0000269|PubMed:12097317, ECO:0000269|PubMed:14522990, ECO:0000269|PubMed:15175427, ECO:0000269|PubMed:15339932}.
• 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: 0.0775

Intolerance Scores

• loftool: 0.948
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.0532
• hipred: Y
• hipred_score: 0.518
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.794

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neil2
• Phenotype: cellular phenotype; normal phenotype; hematopoietic system phenotype; respiratory system phenotype; immune system phenotype

Gene ontology

• Biological process: base-excision repair;nucleotide-excision repair;depyrimidination
• Cellular component: nucleus;nucleoplasm;cytoplasm;spindle microtubule;intracellular membrane-bounded organelle
• Molecular function: damaged DNA binding;DNA-(apurinic or apyrimidinic site) endonuclease activity;protein binding;microtubule binding;zinc ion binding;DNA N-glycosylase activity;class I DNA-(apurinic or apyrimidinic site) endonuclease activity