PIR
Basic information
Region (hg38): X:15384799-15493564
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 PIR 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 | 11 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 4 |
Variants in PIR
This is a list of pathogenic ClinVar variants found in the PIR region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-15385030-T-A | not specified | Uncertain significance (Nov 13, 2023) | ||
| X-15390251-C-T | Benign (Jul 23, 2018) | |||
| X-15397459-A-G | Benign (Jul 04, 2018) | |||
| X-15397526-C-T | not specified | Uncertain significance (Aug 16, 2022) | ||
| X-15407529-G-A | not specified | Uncertain significance (Apr 19, 2024) | ||
| X-15455851-T-C | Uncertain significance (Dec 01, 2023) | |||
| X-15455895-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| X-15455904-G-A | not specified | Uncertain significance (Dec 20, 2022) | ||
| X-15455930-T-C | not specified | Uncertain significance (Sep 07, 2022) | ||
| X-15456011-C-A | Benign (Jul 26, 2018) | |||
| X-15456039-G-A | Benign (Aug 14, 2018) | |||
| X-15459665-C-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| X-15479812-G-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| X-15479820-A-G | not specified | Uncertain significance (Jun 07, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PIR | protein_coding | protein_coding | ENST00000380421 | 9 | 108767 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.34e-10 | 0.0336 | 125681 | 26 | 40 | 125747 | 0.000262 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.398 | 119 | 107 | 1.11 | 0.00000789 | 1895 |
| Missense in Polyphen | 42 | 37.599 | 1.117 | 700 | ||
| Synonymous | -0.0660 | 41 | 40.5 | 1.01 | 0.00000323 | 547 |
| Loss of Function | -0.603 | 13 | 10.9 | 1.20 | 7.35e-7 | 203 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000606 | 0.000570 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000290 | 0.000163 |
| Finnish | 0.000812 | 0.000601 |
| European (Non-Finnish) | 0.000247 | 0.000176 |
| Middle Eastern | 0.000290 | 0.000163 |
| South Asian | 0.000897 | 0.000555 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional coregulator of NF-kappa-B which facilitates binding of NF-kappa-B proteins to target kappa-B genes in a redox-state-dependent manner. May be required for efficient terminal myeloid maturation of hematopoietic cells. Has quercetin 2,3-dioxygenase activity (in vitro). {ECO:0000269|PubMed:17288615, ECO:0000269|PubMed:20010624, ECO:0000269|PubMed:20711196, ECO:0000269|PubMed:23716661}.;
- Pathway
- y branching of actin filaments;Digestion;Digestion and absorption
(Consensus)
Recessive Scores
- pRec
- 0.289
Intolerance Scores
- loftool
- 0.847
- rvis_EVS
- 0.48
- rvis_percentile_EVS
- 79.25
Haploinsufficiency Scores
- pHI
- 0.144
- hipred
- N
- hipred_score
- 0.389
- ghis
- 0.437
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.792
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pir
- Phenotype
- growth/size/body region phenotype; embryo phenotype;
Gene ontology
- Biological process
- transcription by RNA polymerase II;digestion;monocyte differentiation;oxidation-reduction process;regulation of nucleic acid-templated transcription
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- transcription coregulator activity;protein binding;quercetin 2,3-dioxygenase activity;metal ion binding