ALKBH2

alkB homolog 2, alpha-ketoglutarate dependent dioxygenase, the group of Alkylation repair homologs

Basic information

Region (hg38): 12:109088187-109093631

Links

ENSG00000189046 ∙ NCBI:121642 ∙ OMIM:610602 ∙ HGNC:32487 ∙ Uniprot:Q6NS38 ∙ 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 ALKBH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALKBH2 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						0
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in ALKBH2

This is a list of pathogenic ClinVar variants found in the ALKBH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-109088232-G-A		not specified	Uncertain significance (Feb 12, 2024)
12-109088240-A-G		not specified	Uncertain significance (May 16, 2024)
12-109088246-A-G		not specified	Uncertain significance (Jan 24, 2024)
12-109088262-C-T		not specified	Likely benign (Jan 08, 2024)
12-109088303-G-A		not specified	Uncertain significance (Sep 28, 2022)
12-109088307-G-C		not specified	Uncertain significance (Dec 07, 2021)
12-109088335-G-A		not specified	Likely benign (Jan 19, 2024)
12-109088396-T-C		not specified	Uncertain significance (Mar 31, 2023)
12-109088465-C-T		not specified	Uncertain significance (Apr 19, 2023)
12-109090022-C-G		not specified	Uncertain significance (Jun 11, 2024)
12-109090027-T-G		not specified	Uncertain significance (May 24, 2023)
12-109090064-G-A		not specified	Uncertain significance (May 18, 2022)
12-109090135-G-C		not specified	Uncertain significance (Oct 06, 2021)
12-109092581-T-C		not specified	Uncertain significance (Sep 27, 2022)
12-109092639-C-T		not specified	Uncertain significance (Dec 16, 2023)
12-109092755-C-G		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALKBH2	protein_coding	protein_coding	ENST00000429722	3	5441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00327	0.840	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.362	142	155	0.918	0.00000928	1693
Missense in Polyphen		50	52.226	0.95737		597
Synonymous	-0.0113	63	62.9	1.00	0.00000386	542
Loss of Function	1.18	5	8.76	0.570	4.55e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00152	0.00152
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00152	0.00152
South Asian	0.000751	0.000752
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1- ethenoadenine (in vitro). Has strong preference for double- stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. {ECO:0000269|PubMed:12486230, ECO:0000269|PubMed:12594517, ECO:0000269|PubMed:16174769, ECO:0000269|PubMed:18432238, ECO:0000269|PubMed:18519673}.
• Pathway: DNA Repair;ALKBH2 mediated reversal of alkylation damage;Reversal of alkylation damage by DNA dioxygenases;DNA Damage Reversal (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.870
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.310
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Alkbh2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: DNA dealkylation involved in DNA repair;oxidative DNA demethylation;oxidative demethylation;DNA demethylation
• Cellular component: nucleus;nucleoplasm;microtubule cytoskeleton
• Molecular function: ferrous iron binding;DNA-N1-methyladenine dioxygenase activity;cytosine C-5 DNA demethylase activity;1-ethyladenine demethylase activity