NEIL3

nei like DNA glycosylase 3, the group of DNA glycosylases|Zinc fingers RANBP2-type |Zinc fingers GRF-type

Basic information

Region (hg38): 4:177309874-177362936

Links

ENSG00000109674 ∙ NCBI:55247 ∙ OMIM:608934 ∙ HGNC:24573 ∙ Uniprot:Q8TAT5 ∙ 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 NEIL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEIL3 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	4	6
missense			24	3	4	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					5	5
Total	0	0	24	5	13

Variants in NEIL3

This is a list of pathogenic ClinVar variants found in the NEIL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-177309982-A-C		not specified	Uncertain significance (Jul 05, 2023)
4-177309998-C-A		not specified	Benign (Jan 24, 2024)
4-177310010-C-T			Likely benign (May 01, 2024)
4-177310022-G-A			Likely benign (Jul 19, 2018)
4-177310044-G-T		not specified	Uncertain significance (Aug 30, 2021)
4-177310068-G-A		not specified	Uncertain significance (Sep 20, 2023)
4-177310098-G-T		not specified	Uncertain significance (May 06, 2022)
4-177322538-T-G		not specified	Uncertain significance (Apr 16, 2024)
4-177322544-A-G		Low-frequency hearing loss;Low-frequency sensorineural hearing impairment	Uncertain significance (May 13, 2022)
4-177322562-T-G		not specified	Uncertain significance (Jan 23, 2024)
4-177322568-C-A		not specified	Uncertain significance (Feb 16, 2023)
4-177322578-A-C		not specified	Likely benign (Jan 31, 2023)
4-177335697-C-A		not specified	Uncertain significance (May 01, 2024)
4-177335717-T-A		not specified	Uncertain significance (Dec 21, 2022)
4-177335746-A-T		not specified	Uncertain significance (Mar 16, 2024)
4-177335752-G-A		not specified	Uncertain significance (Oct 26, 2022)
4-177335759-C-G		not specified	Benign (Jan 24, 2024)
4-177335766-G-C		not specified	Likely benign (May 31, 2023)
4-177335793-T-G		not specified	Uncertain significance (Oct 04, 2022)
4-177335824-T-TA		not specified	Benign (Jan 24, 2024)
4-177336298-A-G		not specified	Uncertain significance (May 30, 2024)
4-177336313-G-A		not specified	Uncertain significance (May 25, 2022)
4-177336362-G-A		not specified	Benign (Jan 24, 2024)
4-177339718-C-T		not specified	Benign (Jan 24, 2024)
4-177339801-G-A		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEIL3	protein_coding	protein_coding	ENST00000264596	10	53108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-9	0.599	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.148	335	327	1.02	0.0000164	4000
Missense in Polyphen		97	100.82	0.96215		1239
Synonymous	-0.219	118	115	1.03	0.00000566	1119
Loss of Function	1.26	17	23.6	0.721	0.00000107	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.00104
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000310	0.000308
Middle Eastern	0.000109	0.000109
South Asian	0.000441	0.000425
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA glycosylase which prefers single-stranded DNA (ssDNA), or partially ssDNA structures such as bubble and fork structures, to double-stranded DNA (dsDNA). In vitro, displays strong glycosylase activity towards the hydantoin lesions spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh) in both ssDNA and dsDNA; also recognizes FapyA, FapyG, 5-OHU, 5-OHC, 5- OHMH, Tg and 8-oxoA lesions in ssDNA. No activity on 8-oxoG detected. Also shows weak DNA-(apurinic or apyrimidinic site) lyase activity. In vivo, appears to be the primary enzyme involved in removing Sp and Gh from ssDNA in neonatal tissues. Seems to be an important facilitator of cell proliferation in certain populations, for example neural stem/progenitor cells and tumor cells, suggesting a role in replication-associated DNA repair. {ECO:0000269|PubMed:12433996, ECO:0000269|PubMed:19170771, ECO:0000269|PubMed:22569481, ECO:0000269|PubMed:23755964}.
• Pathway: Base excision repair - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0759

Intolerance Scores

• loftool: 0.974
• rvis_EVS: 2.16
• rvis_percentile_EVS: 98.01

Haploinsufficiency Scores

• pHI: 0.0480
• hipred: N
• hipred_score: 0.161

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neil3
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; normal phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: base-excision repair;nucleotide-excision repair
• Cellular component: nucleus;nucleoplasm
• Molecular function: bubble DNA binding;damaged DNA binding;double-stranded DNA binding;single-stranded DNA binding;DNA-(apurinic or apyrimidinic site) endonuclease activity;zinc ion binding;DNA N-glycosylase activity;class I DNA-(apurinic or apyrimidinic site) endonuclease activity