ALKBH5

alkB homolog 5, RNA demethylase, the group of Alkylation repair homologs

Basic information

Region (hg38): 17:18183078-18209954

Previous symbols: [ "OFOXD1" ]

Links

ENSG00000091542 ∙ NCBI:54890 ∙ OMIM:613303 ∙ HGNC:25996 ∙ Uniprot:Q6P6C2 ∙ 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 ALKBH5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALKBH5 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				1		1
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	11	1	0

Variants in ALKBH5

This is a list of pathogenic ClinVar variants found in the ALKBH5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18184290-C-A		not specified	Uncertain significance (Apr 08, 2024)
17-18184296-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-18184469-C-G		not specified	Uncertain significance (Nov 25, 2024)
17-18184521-G-A		not specified	Uncertain significance (Oct 11, 2024)
17-18184544-G-T		not specified	Uncertain significance (Jun 22, 2023)
17-18184568-G-A		not specified	Uncertain significance (Jan 18, 2023)
17-18184578-C-T		not specified	Uncertain significance (Apr 25, 2022)
17-18184604-G-C		not specified	Uncertain significance (Jun 16, 2023)
17-18184635-A-G		not specified	Uncertain significance (Dec 22, 2023)
17-18184680-A-G		not specified	Uncertain significance (Jun 03, 2024)
17-18184813-C-T			Likely benign (Dec 01, 2022)
17-18194973-A-C		not specified	Uncertain significance (Mar 07, 2024)
17-18206880-A-G		not specified	Uncertain significance (Mar 16, 2022)
17-18206889-A-T		not specified	Uncertain significance (Jan 06, 2023)
17-18206931-A-T		not specified	Uncertain significance (Aug 22, 2023)
17-18208304-G-A		not specified	Uncertain significance (Nov 08, 2024)
17-18208389-G-T		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALKBH5	protein_coding	protein_coding	ENST00000399138	4	26877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.950	0.0502	124786	0	3	124789	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	131	244	0.538	0.0000137	2526
Missense in Polyphen		28	109.04	0.25679		1014
Synonymous	-3.97	146	96.4	1.51	0.00000482	819
Loss of Function	3.20	1	13.8	0.0724	6.73e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m6A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes (PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Can also demethylate N(6)- methyladenosine in single-stranded DNA (in vitro) (PubMed:24616105). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:21264265, PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Demethylation of m6A mRNA affects mRNA processing and export (PubMed:23177736). Required for spermatogenesis (By similarity). {ECO:0000250|UniProtKB:Q3TSG4, ECO:0000269|PubMed:21264265, ECO:0000269|PubMed:23177736, ECO:0000269|PubMed:24489119, ECO:0000269|PubMed:24616105, ECO:0000269|PubMed:24778178}.
• Pathway: DNA Repair;Reversal of alkylation damage by DNA dioxygenases;DNA Damage Reversal (Consensus)

Intolerance Scores

• loftool: 0.0348
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.272
• hipred: Y
• hipred_score: 0.728
• ghis: 0.664

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.234

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Alkbh5
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: response to hypoxia;DNA dealkylation involved in DNA repair;mRNA processing;mRNA export from nucleus;spermatogenesis;cell differentiation;oxidative single-stranded RNA demethylation;regulation of mRNA stability
• Cellular component: nucleus;nucleoplasm;Golgi apparatus;cytosol;nuclear speck
• Molecular function: RNA binding;2-oxoglutarate-dependent dioxygenase activity;oxidative RNA demethylase activity;metal ion binding;RNA N6-methyladenosine dioxygenase activity