PIPOX
Basic information
Region (hg38): 17:28950513-29057216
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 18 | 21 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 18 | 3 | 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 |
---|---|---|---|---|
17-28950932-A-G | not specified | Uncertain significance (Jun 18, 2024) | ||
17-28956196-A-G | not specified | Uncertain significance (Jan 26, 2023) | ||
17-28956205-C-T | not specified | Uncertain significance (Sep 11, 2024) | ||
17-28956218-G-A | not specified | Uncertain significance (Jun 17, 2024) | ||
17-28956223-C-T | not specified | Uncertain significance (Apr 04, 2024) | ||
17-28956229-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
17-28956230-G-A | not specified | Uncertain significance (Aug 27, 2024) | ||
17-28956377-A-G | not specified | Uncertain significance (Sep 02, 2024) | ||
17-28956432-C-T | not specified | Uncertain significance (Dec 13, 2022) | ||
17-28956438-G-C | not specified | Uncertain significance (Jul 05, 2023) | ||
17-28956459-C-T | not specified | Uncertain significance (May 28, 2024) | ||
17-28956730-C-T | not specified | Uncertain significance (Aug 26, 2024) | ||
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) | |||
17-28957187-A-T | not specified | Uncertain significance (Mar 15, 2024) | ||
17-28957191-C-T | not specified | Likely benign (Jun 22, 2021) | ||
17-28957350-A-C | not specified | Uncertain significance (Jan 03, 2024) | ||
17-28957366-G-A | not specified | Uncertain significance (Jul 22, 2024) | ||
17-28957425-A-G | Benign (Feb 02, 2021) | |||
17-28957483-G-T | not specified | Uncertain significance (Apr 01, 2024) | ||
17-28957485-C-T | not specified | Uncertain significance (Nov 01, 2022) | ||
17-28957500-C-T | not specified | Uncertain significance (Nov 21, 2023) | ||
17-28957525-C-T | not specified | Uncertain significance (Sep 03, 2024) | ||
17-28957526-G-T | not specified | Uncertain significance (Nov 11, 2024) |
GnomAD
Source:
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:
- 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