GENE REFERENCE / HGNC:16268

PNPLA6

patatin like domain 6, lysophospholipase

protein-coding gene19p13.2Gene information

What does this gene do?

The PNPLA6 gene provides instructions for making a protein called neuropathy target esterase (NTE). The NTE protein is involved in the breakdown of certain fats (lipids). Specifically, NTE breaks down a lipid called lysophosphatidylcholine, which is one of several compounds found in the outer membranes surrounding cells. The correct levels of these compounds are critical to the stability of the cell membranes.

The NTE protein is found most abundantly in the nervous system. It plays an important role in maintaining the stability of the membranes surrounding nerve cells (neurons) and of these cells' specialized extensions, called axons, that transmit nerve impulses. NTE may also play a role in the release of hormones from the pituitary gland, a process that requires particular changes in the cell membrane and appears to involve the lipids found there. The pituitary gland is located at the base of the brain and produces several hormones, including those that help direct sexual development and growth.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-04-01. Source review: 2017-07.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndromeMONDO:0100155 · Evaluated 2023-05-30	Autosomal recessive	DefinitiveSyndromic Disorders Gene Curation Expert Panel
PNPLA6-related spastic paraplegia with or without ataxiaMONDO:0100149 · Evaluated 2022-11-02	Autosomal recessive	DefinitiveSyndromic Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,607
Submissions for variants in or overlapping this gene: 2,699
Submissions explicitly reporting this gene: 2,613
Alleles reported pathogenic / likely pathogenic: 137
VariationIDs with uncertain significance: 584
VariationIDs with conflicting classifications: 103

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about PNPLA6?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 137 alleles in PNPLA6 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in PNPLA6.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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