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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 6.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000264596.4	ENSP00000264596.3	10	yes	-
ENST00000513321.1	ENSP00000424735.1	2	-	-
ENST00000905043.1	ENSP00000575102.1	10	-	-
ENST00000939669.1	ENSP00000609728.1	5	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEIL3 gene.

• not_specified (64 variants)
• not_provided (5 variants)
• Low-frequency_sensorineural_hearing_impairment (1 variants)
• Low-frequency_hearing_loss (1 variants)

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. These statistics are base on transcript: NM_000018248.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	3		4
missense			66	5		71
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	69	8	0

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
		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

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

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