GeneBe

ALKBH2

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

Basic information

Region (hg38): 12:109088188-109093631

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.

  • not_specified (42 variants)

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. These statistics are base on transcript: NM_001145374.2. 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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
 6
missense
33
clinvar
3
clinvar
 36
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 33 9 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ALKBH2protein_codingprotein_codingENST00000429722 35441
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.003270.8401256790691257480.000274
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3621421550.9180.000009281693
Missense in Polyphen5052.2260.95737597
Synonymous-0.01136362.91.000.00000386542
Loss of Function1.1858.760.5704.55e-7105

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001810.000181
Ashkenazi Jewish0.00009920.0000992
East Asian0.001520.00152
Finnish0.000.00
European (Non-Finnish)0.0001160.000114
Middle Eastern0.001520.00152
South Asian0.0007510.000752
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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