PIPOX

protein-coding

pipecolic acid and sarcosine oxidase

Gene summary

Enables L-pipecolate oxidase activity and sarcosine oxidase activity. Involved in obsolete L-lysine catabolic process to acetyl-CoA via L-pipecolate. Located in peroxisome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016518.3

Inheritance

—

ClinVar variants

U:56B:5

Top phenotype

Low-frequency sensorineural hearing impairment

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr17:28,950,513-29,057,216

External References & Databases

Ensembl (ENSG00000179761)

Transcript & Mutation Effects

hg38 • Region Span ~106.7 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 PIPOX variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 58

Low-frequency sensorineural hearing impairmentTotal: 1

Low-frequency hearing lossTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016518.3. 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			1 clinvar	1 clinvar		2
missense			54 clinvar	4 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	56	5	0	61

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016518.3	RefSeq	NP_057602.2	8	MANE Select
ENST00000323372.9	Ensembl	ENSP00000317721.4	8	MANE Select
ENST00000466889.5	Ensembl	ENSP00000465428.1	3	Standard
ENST00000469082.1	Ensembl	ENSP00000465329.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lysine degradation - Homo sapiens (human)
Peroxisome - Homo sapiens (human)
Glycine, serine and threonine metabolism - Homo sapiens (human)
Lysine Degradation
Hyperlysinemia I, Familial

Biological Process

lysine catabolic process
protein targeting to peroxisome
L-lysine catabolic process to acetyl-CoA via L-pipecolate
tetrahydrofolate metabolic process
oxidation-reduction process

Molecular Function

signaling receptor binding
protein binding
sarcosine oxidase activity
L-pipecolate oxidase activity

Cellular Component

peroxisome
peroxisomal matrix
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323372
Coding exons: 8
Length: 106704
Individuals with no LoFs: 125688
Homozygous LoFs: 1
Heterozygous LoFs: 59
Defined: 125748
p: 0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.237	224	234	0.956	0.0000139	2527
Missense (PolyPhen)		54	59.688	0.9047		606
Synonymous	0.756	83	92.2	0.900	0.00000552	782
Loss of Function	0.608	19	22.1	0.860	0.00000126	229

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00014	0.000092	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00066	0.00065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Metabolizes sarcosine, L-pipecolic acid and L-proline.;

Recessive Scores

pRec: 0.152

Intolerance Scores

LoFtool: 0.428
RVIS EVS: -0.56
RVIS percentile EVS: 19.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.748

Gene Damage Prediction

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