ALKBH4

alkB homolog 4, lysine demethylase, the group of Alkylation repair homologs

Basic information

Region (hg38): 7:102456238-102464863

Links

ENSG00000160993 ∙ NCBI:54784 ∙ OMIM:613302 ∙ HGNC:21900 ∙ Uniprot:Q9NXW9 ∙ 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 ALKBH4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALKBH4 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in ALKBH4

This is a list of pathogenic ClinVar variants found in the ALKBH4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-102457492-G-A		not specified	Uncertain significance (Jan 30, 2024)
7-102457497-G-T		not specified	Uncertain significance (May 31, 2023)
7-102457507-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-102457513-G-T		not specified	Uncertain significance (May 31, 2023)
7-102457519-C-G		not specified	Uncertain significance (Apr 25, 2022)
7-102457521-A-G		not specified	Uncertain significance (Dec 13, 2022)
7-102457530-C-T		not specified	Uncertain significance (Jan 26, 2022)
7-102457533-T-C		not specified	Uncertain significance (Jun 17, 2024)
7-102457558-G-A		not specified	Uncertain significance (Feb 23, 2023)
7-102457567-C-G		not specified	Uncertain significance (Oct 05, 2023)
7-102457590-G-A		not specified	Uncertain significance (May 29, 2024)
7-102457684-G-A		not specified	Uncertain significance (Jan 25, 2023)
7-102457689-G-A		not specified	Likely benign (Oct 05, 2023)
7-102457741-G-A		not specified	Uncertain significance (Sep 06, 2022)
7-102457775-C-G		not specified	Uncertain significance (Mar 21, 2024)
7-102457819-G-A		not specified	Uncertain significance (Jan 17, 2024)
7-102457843-A-G		not specified	Uncertain significance (Dec 21, 2022)
7-102457849-C-T		not specified	Uncertain significance (Jul 09, 2021)
7-102457905-C-T		not specified	Uncertain significance (Jun 07, 2023)
7-102457906-G-A		not specified	Uncertain significance (Mar 17, 2023)
7-102457929-A-G		not specified	Uncertain significance (Nov 28, 2023)
7-102457936-C-G		not specified	Uncertain significance (Aug 02, 2021)
7-102457936-C-T		not specified	Uncertain significance (Jun 13, 2022)
7-102459615-G-A		not specified	Uncertain significance (Jan 20, 2023)
7-102459644-C-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALKBH4	protein_coding	protein_coding	ENST00000292566	3	8639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.126	0.853	124835	0	6	124841	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.562	181	204	0.889	0.0000143	1890
Missense in Polyphen		57	63.731	0.89438		610
Synonymous	-1.11	106	92.4	1.15	0.00000661	657
Loss of Function	1.99	3	9.66	0.310	4.13e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000597	0.0000597
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000205	0.0000178
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dioxygenase that mediates demethylation of actin monomethylated at 'Lys-84' (K84me1), thereby acting as a regulator of actomyosin-processes. Demethylation of actin K84me1 is required for maintaining actomyosin dynamics supporting normal cleavage furrow ingression during cytokinesis and cell migration. May be involved in transcription regulation. {ECO:0000269|PubMed:21166655, ECO:0000269|PubMed:23673617}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.201
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.338
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.385

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Alkbh4
• Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: protein demethylation;actomyosin structure organization;cleavage furrow ingression;oxidation-reduction process;oxidative demethylation
• Cellular component: nucleus;cytoplasm;midbody;contractile ring
• Molecular function: actin binding;protein binding;oxidoreductase activity;2-oxoglutarate-dependent dioxygenase activity;demethylase activity;metal ion binding