ETNPPL

ethanolamine-phosphate phospho-lyase

Basic information

Region (hg38): 4:108742048-108763054

Previous symbols: [ "AGXT2L1" ]

Links

ENSG00000164089 ∙ NCBI:64850 ∙ OMIM:614682 ∙ HGNC:14404 ∙ Uniprot:Q8TBG4 ∙ 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 ETNPPL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETNPPL 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in ETNPPL

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

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

Position	Type	Phenotype	Significance	ClinVar
4-108742489-T-G		not specified	Uncertain significance (Dec 06, 2022)
4-108742495-G-A		not specified	Uncertain significance (Feb 11, 2025)
4-108742499-C-G		not specified	Uncertain significance (Dec 05, 2022)
4-108742500-T-C		not specified	Uncertain significance (Aug 10, 2024)
4-108742528-A-T		not specified	Uncertain significance (May 26, 2024)
4-108742582-T-C		not specified	Uncertain significance (Oct 26, 2022)
4-108742602-T-G		not specified	Uncertain significance (May 30, 2022)
4-108746780-G-A		not specified	Uncertain significance (Sep 14, 2022)
4-108746835-T-C		not specified	Uncertain significance (Aug 17, 2022)
4-108748011-T-C		not specified	Uncertain significance (Jun 18, 2021)
4-108748020-A-G		not specified	Uncertain significance (May 09, 2023)
4-108748069-C-A		not specified	Uncertain significance (May 02, 2024)
4-108749239-G-A		not specified	Uncertain significance (Jan 30, 2024)
4-108749261-A-G		not specified	Uncertain significance (Sep 08, 2024)
4-108749264-T-A		not specified	Uncertain significance (May 25, 2022)
4-108749264-T-G		not specified	Uncertain significance (Jan 09, 2025)
4-108749272-G-A		not specified	Uncertain significance (Aug 27, 2024)
4-108749313-G-C		not specified	Uncertain significance (Jan 24, 2024)
4-108749339-T-C		not specified	Uncertain significance (May 11, 2022)
4-108749368-C-T		not specified	Uncertain significance (Jul 02, 2024)
4-108751009-A-C		not specified	Uncertain significance (Nov 08, 2024)
4-108752908-T-C		not specified	Likely benign (Mar 14, 2023)
4-108752918-C-G		not specified	Uncertain significance (Dec 04, 2024)
4-108752987-C-T		not specified	Uncertain significance (Jul 05, 2023)
4-108753008-G-T		not specified	Uncertain significance (Apr 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETNPPL	protein_coding	protein_coding	ENST00000296486	13	21015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000751	0.996	125697	1	50	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	194	275	0.707	0.0000136	3309
Missense in Polyphen		52	108.07	0.48117		1257
Synonymous	-0.925	110	98.3	1.12	0.00000548	918
Loss of Function	2.55	11	24.7	0.446	0.00000120	315

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000380	0.000369
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000999	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the pyridoxal-phosphate-dependent breakdown of phosphoethanolamine, converting it to ammonia, inorganic phosphate and acetaldehyde. {ECO:0000269|PubMed:22241472}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Synthesis of PE;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.0975
• hipred: N
• hipred_score: 0.421
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etnppl

Zebrafish Information Network

• Gene name: etnppl
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: phosphatidylethanolamine biosynthetic process
• Cellular component: cellular_component;mitochondrial matrix
• Molecular function: transaminase activity;pyridoxal phosphate binding;ethanolamine-phosphate phospho-lyase activity