ETNK2

ethanolamine kinase 2

Basic information

Region (hg38): 1:204131062-204152044

Links

ENSG00000143845 ∙ NCBI:55224 ∙ OMIM:609859 ∙ HGNC:25575 ∙ Uniprot:Q9NVF9 ∙ 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 ETNK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETNK2 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	17	2	1

Variants in ETNK2

This is a list of pathogenic ClinVar variants found in the ETNK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-204132194-A-T		not specified	Uncertain significance (Nov 30, 2022)
1-204134577-G-C		not specified	Uncertain significance (May 23, 2023)
1-204137163-T-A		not specified	Uncertain significance (Jul 26, 2021)
1-204137188-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-204137209-C-G			Likely benign (Feb 01, 2023)
1-204140113-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-204141373-A-C			Benign (Apr 24, 2018)
1-204141420-G-A		not specified	Uncertain significance (Jun 05, 2023)
1-204141428-A-G		not specified	Uncertain significance (Dec 31, 2023)
1-204141455-A-G		not specified	Uncertain significance (Nov 14, 2023)
1-204146730-T-C		not specified	Uncertain significance (Jan 18, 2022)
1-204146764-C-T		not specified	Likely benign (Aug 15, 2023)
1-204149722-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-204149805-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-204149910-T-C		not specified	Uncertain significance (Jan 04, 2022)
1-204151669-C-T		not specified	Uncertain significance (Apr 09, 2024)
1-204151717-G-A		not specified	Uncertain significance (Aug 01, 2022)
1-204151720-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-204151735-G-C		not specified	Uncertain significance (Jul 26, 2022)
1-204151819-C-A		not specified	Likely benign (Feb 06, 2024)
1-204151825-G-T		not specified	Uncertain significance (Dec 15, 2021)
1-204151840-G-C		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETNK2	protein_coding	protein_coding	ENST00000367202	8	21118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.81e-7	0.787	125596	0	13	125609	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	170	215	0.790	0.0000122	2503
Missense in Polyphen		63	79.508	0.79238		950
Synonymous	0.119	88	89.4	0.984	0.00000529	712
Loss of Function	1.33	12	18.1	0.663	7.70e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000714	0.0000705
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Highly specific for ethanolamine phosphorylation. Does not have choline kinase activity (By similarity). {ECO:0000250}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Metabolism of lipids;Metabolism;Synthesis of PE;phosphatidylethanolamine biosynthesis II;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0835

Intolerance Scores

• loftool: 0.342
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.0800
• hipred: N
• hipred_score: 0.231
• ghis: 0.382

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etnk2
• Phenotype: reproductive system phenotype; normal phenotype; cellular phenotype

Gene ontology

• Biological process: in utero embryonic development;placenta development;phosphatidylethanolamine biosynthetic process;biological_process;post-embryonic development;phosphorylation;multicellular organism growth
• Cellular component: cellular_component;cytosol
• Molecular function: ethanolamine kinase activity;ATP binding