POMP
proteasome maturation protein
Basic information
Region (hg38): 13:28659065-28678959
Previous symbols: [ "C13orf12" ]
Links
Phenotypes
GenCC
Source:
- keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (Limited), mode of inheritance: AR
- keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (Moderate), mode of inheritance: AR
- proteasome-associated autoinflammatory syndrome 2 (Moderate), mode of inheritance: AD
- keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (Strong), mode of inheritance: AR
- keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (Supportive), mode of inheritance: AR
- proteasome-associated autoinflammatory syndrome 2 (Strong), mode of inheritance: AD
- keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Proteasome-associated autoinflammatory syndrome 2 | AD | Allergy/Immunology/Infectious | Individuals have been described with recurrent infections, and awareness may allow preventative measures and early and aggressive treatment of infections; HSCT has been described | Allergy/Immunology/Infectious; Craniofacial; Dermatologic; Musculoskeletal | 12022327; 20226437; 26524591; 29805043 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (106 variants)
- Inborn_genetic_diseases (20 variants)
- Proteasome-associated_autoinflammatory_syndrome_2 (5 variants)
- POMP-related_disorder (4 variants)
- Keratosis_linearis-ichthyosis_congenita-sclerosing_keratoderma_syndrome (3 variants)
- not_specified (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the POMP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015932.6. 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 | 19 | 20 | ||||
| missense | 52 | 53 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 4 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 4 | 1 | 54 | 19 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| POMP | protein_coding | protein_coding | ENST00000380842 | 6 | 19822 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.909 | 0.0900 | 122223 | 0 | 1 | 122224 | 0.00000409 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.966 | 49 | 72.1 | 0.680 | 0.00000354 | 923 |
| Missense in Polyphen | 7 | 14.424 | 0.48531 | 189 | ||
| Synonymous | -0.118 | 26 | 25.2 | 1.03 | 0.00000125 | 263 |
| Loss of Function | 2.58 | 0 | 7.74 | 0.00 | 3.26e-7 | 101 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000295 | 0.0000295 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Molecular chaperone essential for the assembly of standard proteasomes and immunoproteasomes. Degraded after completion of proteasome maturation. Mediates the association of 20S preproteasome with the endoplasmic reticulum. {ECO:0000269|PubMed:15944226, ECO:0000269|PubMed:16251969, ECO:0000269|PubMed:17948026}.;
- Disease
- DISEASE: Keratosis linearis with ichthyosis congenita and sclerosing keratoderma (KLICK) [MIM:601952]: A keratinizing disorder characterized by ichthyosis, palmoplantar keratoderma with constricting bands around fingers, flexural deformities of fingers and keratotic papules in a linear distribution on the flexural side of large joints. Histological examination of the skin of affected individuals shows hypertrophy and hyperplasia of the spinous, granular and horny epidermal layer. {ECO:0000269|PubMed:20226437}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Proteasome - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.275
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.675
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.508
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pomp
- Phenotype
Gene ontology
- Biological process
- proteasome assembly
- Cellular component
- nucleus;cytoplasm;endoplasmic reticulum;cytosol;nuclear speck;organelle membrane
- Molecular function
- protein binding