PIPOX

pipecolic acid and sarcosine oxidase

Basic information

Region (hg38): 17:28950513-29057216

Links

ENSG00000179761

∙ NCBI:51268 ∙ OMIM:616713 ∙ HGNC:17804 ∙ Uniprot:Q9P0Z9 ∙ 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 PIPOX gene.

not_specified (49 variants)
Low-frequency_sensorineural_hearing_impairment (1 variants)
Low-frequency_hearing_loss (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIPOX gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016518.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			46 clinvar	3 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	4	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIPOX	protein_coding	protein_coding	ENST00000323372	8	106704

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.64e-12	0.125	125688	1	59	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.237	224	234	0.956	0.0000139	2527
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000543	0.000543
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.0000924
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000655	0.000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Metabolizes sarcosine, L-pipecolic acid and L-proline.;
Pathway: Lysine degradation - Homo sapiens (human);Peroxisome - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);Lysine Degradation;Hyperlysinemia I, Familial;2-aminoadipic 2-oxoadipic aciduria;Pyridoxine dependency with seizures;Saccharopinuria/Hyperlysinemia II;Glutaric Aciduria Type I;Hyperlysinemia II or Saccharopinuria;Lysine catabolism;Metabolism of proteins;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Glycine Serine metabolism;Metabolism;Peroxisomal protein import;Lysine metabolism;lysine degradation II (pipecolate pathway);Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

pRec: 0.152

Intolerance Scores

loftool: 0.428
rvis_EVS: -0.56
rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

pHI: 0.932
hipred: N
hipred_score: 0.205
ghis: 0.461

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.748

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pipox
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); limbs/digits/tail phenotype;

Gene ontology

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
Cellular component: peroxisome;peroxisomal matrix;cytosol
Molecular function: signaling receptor binding;protein binding;sarcosine oxidase activity;L-pipecolate oxidase activity