ALPK2

alpha kinase 2, the group of I-set domain containing

Basic information

Region (hg38): 18:58481247-58629091

Links

ENSG00000198796 ∙ NCBI:115701 ∙ OMIM:619965 ∙ HGNC:20565 ∙ Uniprot:Q86TB3 ∙ 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 ALPK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALPK2 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				897	18	915
missense			1638	103	30	1771
nonsense						0
start loss						0
frameshift						0
inframe indel				1	2	3
splice donor/acceptor (+/-2bp)						0
splice region				5	3	8
non coding					2	2
Total	0	0	1638	1001	52

Variants in ALPK2

This is a list of pathogenic ClinVar variants found in the ALPK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-58481816-A-G		ALPK2-related disorder	Benign (Oct 17, 2019)
18-58481829-T-A		not specified	Uncertain significance (Sep 03, 2022)
18-58481835-T-A		not specified	Uncertain significance (Aug 22, 2022)
18-58481836-T-G		not specified	Uncertain significance (Jan 10, 2022)
18-58481837-C-T		not specified	Uncertain significance (Mar 10, 2023)
18-58481838-G-A		not specified	Likely benign (Feb 13, 2022)
18-58481838-G-C		not specified	Likely benign (Feb 21, 2022)
18-58481838-G-T		not specified	Likely benign (Mar 03, 2022)
18-58481839-C-T		not specified	Uncertain significance (Jun 19, 2024)
18-58481844-G-A		not specified	Likely benign (Sep 26, 2019)
18-58481845-G-A		not specified	Uncertain significance (Sep 14, 2021)
18-58481849-C-G		not specified	Uncertain significance (Apr 28, 2024)
18-58481850-A-G		ALPK2-related disorder • not specified	Likely benign (Feb 26, 2022)
18-58481852-G-A		not specified	Likely benign (Dec 01, 2022)
18-58481853-C-T		not specified	Likely benign (Feb 22, 2022)
18-58481854-C-T		not specified	Uncertain significance (Apr 30, 2024)
18-58481855-C-G		not specified	Uncertain significance (Jul 03, 2023)
18-58481857-G-T		not specified	Uncertain significance (Jul 08, 2021)
18-58481858-C-T		not specified	Likely benign (Apr 29, 2022)
18-58481862-C-G		not specified	Uncertain significance (Nov 24, 2022)
18-58481863-T-C		not specified	Uncertain significance (May 14, 2024)
18-58481864-T-C		not specified	Uncertain significance (Oct 29, 2021)
18-58481866-A-G		not specified	Uncertain significance (Apr 20, 2022)
18-58481866-A-T		not specified	Uncertain significance (Nov 09, 2023)
18-58481867-T-C		ALPK2-related disorder	Benign (Oct 17, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALPK2	protein_coding	protein_coding	ENST00000361673	12	147711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-21	0.985	125640	0	107	125747	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.406	1084	1.12e+3	0.966	0.0000580	14256
Missense in Polyphen		248	244.11	1.0159		3254
Synonymous	-0.251	444	437	1.02	0.0000249	4232
Loss of Function	2.84	45	70.8	0.635	0.00000326	989

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000482	0.000481
Ashkenazi Jewish	0.00403	0.00398
East Asian	0.000171	0.000163
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000171	0.000163
South Asian	0.000792	0.000784
Other	0.000671	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Kinase that recognizes phosphorylation sites in which the surrounding peptides have an alpha-helical conformation.

Recessive Scores

• pRec: 0.0748

Intolerance Scores

• loftool: 0.966
• rvis_EVS: 4.93
• rvis_percentile_EVS: 99.8

Haploinsufficiency Scores

• pHI: 0.0357
• hipred: N
• hipred_score: 0.145
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0375

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Alpk2

Zebrafish Information Network

• Gene name: alpk2
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein phosphorylation
• Molecular function: protein serine/threonine kinase activity;ATP binding