ALKBH6

alkB homolog 6, the group of Alkylation repair homologs

Basic information

Region (hg38): 19:36009120-36014239

Links

ENSG00000239382 ∙ NCBI:84964 ∙ OMIM:613304 ∙ HGNC:28243 ∙ Uniprot:Q3KRA9 ∙ 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 ALKBH6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALKBH6 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	11	0	0

Variants in ALKBH6

This is a list of pathogenic ClinVar variants found in the ALKBH6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-36009355-G-C		not specified	Uncertain significance (Oct 05, 2022)
19-36009408-T-G		not specified	Uncertain significance (Sep 06, 2022)
19-36009486-C-T		not specified	Uncertain significance (Jun 13, 2024)
19-36009508-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-36010577-G-T		not specified	Uncertain significance (May 17, 2023)
19-36010584-C-T		not specified	Uncertain significance (Feb 02, 2023)
19-36010588-C-T		not specified	Likely benign (May 24, 2024)
19-36010596-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-36010614-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-36010677-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-36010946-A-G		not specified	Uncertain significance (Oct 10, 2023)
19-36010955-A-G		not specified	Uncertain significance (Feb 17, 2024)
19-36014181-C-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALKBH6	protein_coding	protein_coding	ENST00000378875	7	5120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.106	0.888	125730	1	10	125741	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	85	121	0.704	0.00000704	1653
Missense in Polyphen		23	48.308	0.47611		686
Synonymous	1.40	38	50.6	0.750	0.00000327	588
Loss of Function	2.40	4	13.5	0.296	7.27e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000917	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000565	0.0000544
Finnish	0.0000515	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000565	0.0000544
South Asian	0.000101	0.0000980
Other	0.000337	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable dioxygenase that requires molecular oxygen, alpha-ketoglutarate and iron. {ECO:0000250}.

Recessive Scores

• pRec: 0.106

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.580
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Alkbh6

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: nucleus;nucleoplasm;cytoplasm;focal adhesion
• Molecular function: protein binding;metal ion binding;dioxygenase activity