PIPOX

pipecolic acid and sarcosine oxidase

Basic information

Region (hg38): 17:28950512-29057216

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.

• Inborn genetic diseases (16 variants)
• Low-frequency hearing loss;Low-frequency sensorineural hearing impairment (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.

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						0
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in PIPOX

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

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

Position	Type	Phenotype	Significance	ClinVar
17-28956196-A-G		not specified	Uncertain significance (Jan 26, 2023)
17-28956218-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-28956229-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-28956230-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-28956432-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-28956438-G-C		not specified	Uncertain significance (Jul 05, 2023)
17-28956734-T-C		not specified	Likely benign (Jan 31, 2022)
17-28957076-A-G			Benign (Jul 11, 2017)
17-28957176-T-C			Benign (Dec 31, 2019)
17-28957191-C-T		not specified	Likely benign (Jun 22, 2021)
17-28957350-A-C		not specified	Uncertain significance (Jan 03, 2024)
17-28957425-A-G			Benign (Feb 02, 2021)
17-28957485-C-T		not specified	Uncertain significance (Nov 01, 2022)
17-28957500-C-T		not specified	Uncertain significance (Nov 21, 2023)
17-28957548-AG-A			Benign (Feb 02, 2021)
17-28957966-G-T		not specified	Uncertain significance (Apr 13, 2023)
17-28957984-G-C		not specified	Uncertain significance (Apr 19, 2023)
17-28958117-G-A		not specified	Uncertain significance (Jun 29, 2022)
17-28958132-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-28958133-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-28959040-C-T		Nonsyndromic hearing impairment	Uncertain significance (-)
17-28959135-C-T			Benign (Dec 31, 2019)
17-28959337-C-T		not specified	Uncertain significance (Jan 04, 2024)
17-28959404-C-T			Benign (Dec 31, 2018)
17-28959444-C-T			Benign (Dec 31, 2019)

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