ALKBH7
protein-codingalkB homolog 7, the group of Alkylation repair homologs
Gene summary
Enables tRNA demethylase activity. Involved in DNA damage response; oxidative RNA demethylation; and regulation of mitochondrial membrane permeability involved in programmed necrotic cell death. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Jun 2026]
- SPATA11
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ALKBH7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032306.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 50 | 50 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 51 | 0 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115682.1 | 4 | MANE Select | |
| Ensembl | ENSP00000245812.2 | 4 | MANE Select | |
| Ensembl | ENSP00000470542.1 | 2 | Standard | |
| Ensembl | ENSP00000470542.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- fatty acid metabolic process
- cellular response to DNA damage stimulus
- regulation of lipid storage
- oxidation-reduction process
- regulation of mitochondrial membrane permeability involved in programmed necrotic cell death
Molecular Function
- metal ion binding
- dioxygenase activity
Cellular Component
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000245812
- Coding exons
- 4
- Length
- 2599
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 31
- Defined
- 125709
- p
- 0.000123
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.126 | 147 | 151 | 0.971 | 0.0000103 | 1366 |
| Missense (PolyPhen) | 60 | 61.412 | 0.97701 | 557 | ||
| Synonymous | 0.673 | 61 | 68.1 | 0.896 | 0.00000454 | 506 |
| Loss of Function | 0.117 | 9 | 9.39 | 0.959 | 4.92e-7 | 87 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00020 | 0.00019 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May function as protein hydroxylase; can catalyze auto- hydroxylation at Leu-110 (in vitro), but this activity may be due to the absence of the true substrate (PubMed:25122757). Required to induce programmed necrosis in response to DNA damage caused by cytotoxic alkylating agents. Acts by triggering the collapse of mitochondrial membrane potential and loss of mitochondrial function that leads to energy depletion and cell death (PubMed:23666923). ALKBH7-mediated necrosis is probably required to prevent the accumulation of cells with DNA damage (PubMed:23666923). Does not display DNA demethylase activity (PubMed:23666923). Involved in fatty acid metabolism (By similarity). {ECO:0000250|UniProtKB:Q9D6Z0, ECO:0000269|PubMed:23666923, ECO:0000269|PubMed:25122757}.;
Recessive Scores
- pRec
- 0.0963
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.757
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |