ETNPPL

protein-coding

ethanolamine-phosphate phospho-lyase

Gene summary

Enables ethanolamine-phosphate phospho-lyase activity. Predicted to act upstream of or within several processes, including cellular response to glucocorticoid stimulus; ceramide phosphoethanolamine catabolic process; and phospholipid transfer to membrane. Predicted to be located in mitochondrial matrix. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

AGXT2L1

MANE transcript

NM_031279.4

Inheritance

—

ClinVar variants

U:61B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr4:108,742,048-108,763,054

External References & Databases

Ensembl (ENSG00000164089)

Transcript & Mutation Effects

hg38 • Region Span ~21.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ETNPPL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031279.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			56 clinvar	2 clinvar		58
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	61	3	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031279.4	RefSeq	NP_112569.2	13	MANE Select
ENST00000296486.8	Ensembl	ENSP00000296486.3	13	MANE Select
NM_001146590.2	RefSeq	NP_001140062.1	13	Standard
NM_001146627.2	RefSeq	NP_001140099.1	12	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
etnppl	Danio rerio	Structure: blood cell Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

etnppl

Danio rerio

Structure: blood cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerophospholipid metabolism - Homo sapiens (human)
Metabolism of lipids
Metabolism
Synthesis of PE
Glycerophospholipid biosynthesis

Biological Process

phosphatidylethanolamine biosynthetic process

Molecular Function

transaminase activity
pyridoxal phosphate binding
ethanolamine-phosphate phospho-lyase activity

Cellular Component

cellular_component
mitochondrial matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296486
Coding exons: 13
Length: 21015
Individuals with no LoFs: 125697
Homozygous LoFs: 1
Heterozygous LoFs: 50
Defined: 125748
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.73	194	275	0.707	0.0000136	3309
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00038	0.00037	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the pyridoxal-phosphate-dependent breakdown of phosphoethanolamine, converting it to ammonia, inorganic phosphate and acetaldehyde. {ECO:0000269|PubMed:22241472}.;

Recessive Scores

pRec: 0.170

Intolerance Scores

RVIS EVS: 0
RVIS percentile EVS: 53.85

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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