CHKA

choline kinase alpha

Basic information

Region (hg38): 11:68052859-68121444

Previous symbols: [ "CHK" ]

Links

ENSG00000110721 ∙ NCBI:1119 ∙ OMIM:118491 ∙ HGNC:1937 ∙ Uniprot:P35790 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures (Limited), mode of inheritance: AR
• neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures (Strong), mode of inheritance: AR
• neurodevelopmental disorder (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	35202461

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHKA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHKA 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		3	29	1		33
nonsense						0
start loss			1			1
frameshift		1				1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	4	31	2	0

Variants in CHKA

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

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

Position	Type	Phenotype	Significance	ClinVar
11-68054006-C-A		not specified	Uncertain significance (Nov 07, 2024)
11-68061977-A-G			Likely benign (Mar 01, 2023)
11-68064604-C-T		not specified	Uncertain significance (Aug 30, 2021)
11-68065890-A-G		Seizure;Intellectual disability, severe;Microcephaly • Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures	Likely pathogenic (Aug 08, 2024)
11-68066469-G-T		not specified	Uncertain significance (Feb 28, 2024)
11-68066483-G-C		not specified	Uncertain significance (Sep 06, 2024)
11-68066492-C-T		not specified	Likely benign (Jul 02, 2024)
11-68068914-G-C		not specified	Uncertain significance (Dec 02, 2024)
11-68070196-T-A		not specified	Uncertain significance (Apr 04, 2024)
11-68070216-T-C		not specified	Uncertain significance (Dec 01, 2022)
11-68070245-A-C		not specified	Uncertain significance (Nov 23, 2022)
11-68070752-G-A		not specified	Uncertain significance (Sep 10, 2024)
11-68070768-C-G		not specified	Uncertain significance (May 23, 2023)
11-68070800-C-T		Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures	Uncertain significance (Nov 22, 2023)
11-68070845-C-T		not specified	Uncertain significance (Sep 07, 2022)
11-68074767-G-A		Seizure;Intellectual disability, severe;Microcephaly • Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures	Likely pathogenic (Oct 15, 2021)
11-68074785-C-T		not specified	Uncertain significance (Dec 13, 2022)
11-68074799-A-G		not specified	Uncertain significance (Aug 22, 2023)
11-68097060-G-A		Seizure;Intellectual disability, severe;Microcephaly • Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures	Likely pathogenic (Oct 15, 2021)
11-68120868-G-C		not specified	Uncertain significance (Aug 07, 2024)
11-68120925-G-A		not specified	Uncertain significance (May 09, 2022)
11-68120954-G-A		not specified	Uncertain significance (May 08, 2023)
11-68120964-G-A		not specified	Uncertain significance (Dec 14, 2021)
11-68120965-C-G		not specified	Uncertain significance (Sep 21, 2023)
11-68120968-GGGCAGC-G		Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHKA	protein_coding	protein_coding	ENST00000265689	12	68586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.227	0.772	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	163	203	0.802	0.0000103	2986
Missense in Polyphen		50	89.472	0.55883		1284
Synonymous	0.740	68	76.2	0.892	0.00000409	854
Loss of Function	3.49	6	24.7	0.243	0.00000130	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000107	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a key role in phospholipid biosynthesis and may contribute to tumor cell growth. Catalyzes the first step in phosphatidylcholine biosynthesis. Contributes to phosphatidylethanolamine biosynthesis. Phosphorylates choline and ethanolamine. Has higher activity with choline. {ECO:0000269|PubMed:19915674}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Phospholipid Biosynthesis;Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Acetylcholine Synthesis;Metabolism of lipids;phosphatidylcholine biosynthesis;Metabolism;Synthesis of PC;Synthesis of PE;phosphatidylcholine biosynthesis pathway;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.261

Intolerance Scores

• loftool: 0.603
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.210
• hipred: Y
• hipred_score: 0.728
• ghis: 0.562

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chka
• Phenotype: homeostasis/metabolism phenotype; liver/biliary system 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: ethanolamine metabolic process;lipid metabolic process;phosphatidylethanolamine biosynthetic process;phosphatidylcholine biosynthetic process;CDP-choline pathway;lipid transport;response to toxic substance;phosphorylation;choline metabolic process;response to 3-methylcholanthrene
• Cellular component: cytosol
• Molecular function: choline kinase activity;cholinesterase activity;ethanolamine kinase activity;ATP binding;drug binding;choline binding;protein homodimerization activity