RPN1
ribophorin I, the group of Oligosaccharyltransferase complex subunits
Basic information
Region (hg38): 3:128619968-128681075
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (6 variants)
- not provided (4 variants)
- Hereditary breast ovarian cancer syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPN1 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | 2 | ||||
missense | 7 | 1 | 8 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 7 | 0 | 4 |
Variants in RPN1
This is a list of pathogenic ClinVar variants found in the RPN1 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-128620541-G-A | Inborn genetic diseases | Uncertain significance (Feb 22, 2023) | ||
3-128620588-G-A | Benign (Apr 30, 2018) | |||
3-128622232-C-G | Inborn genetic diseases | Uncertain significance (Jan 23, 2023) | ||
3-128622303-T-C | Inborn genetic diseases | Uncertain significance (Jun 06, 2023) | ||
3-128625535-T-C | Benign (Apr 30, 2018) | |||
3-128625589-T-C | Inborn genetic diseases | Uncertain significance (Dec 19, 2022) | ||
3-128625917-G-T | Inborn genetic diseases | Uncertain significance (Aug 16, 2022) | ||
3-128625978-G-A | Inborn genetic diseases | Uncertain significance (Mar 17, 2023) | ||
3-128630091-T-C | Inborn genetic diseases | Uncertain significance (Jan 18, 2023) | ||
3-128632025-C-G | Inborn genetic diseases | Uncertain significance (Jul 19, 2023) | ||
3-128632079-G-A | Hereditary breast ovarian cancer syndrome | Uncertain significance (Aug 01, 2020) | ||
3-128637793-G-A | Benign (Jun 01, 2018) | |||
3-128637856-C-T | Benign (Apr 30, 2018) | |||
3-128637893-C-T | Inborn genetic diseases | Uncertain significance (Nov 09, 2021) | ||
3-128644979-T-C | Inborn genetic diseases | Uncertain significance (Oct 04, 2022) | ||
3-128650748-G-A | Inborn genetic diseases | Uncertain significance (Dec 21, 2022) | ||
3-128650793-G-A | Inborn genetic diseases | Uncertain significance (Oct 12, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPN1 | protein_coding | protein_coding | ENST00000296255 | 10 | 61102 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.239 | 0.761 | 125733 | 0 | 15 | 125748 | 0.0000596 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.736 | 305 | 343 | 0.888 | 0.0000188 | 3939 |
Missense in Polyphen | 80 | 103.91 | 0.76986 | 1243 | ||
Synonymous | -0.0772 | 141 | 140 | 1.01 | 0.00000750 | 1243 |
Loss of Function | 3.51 | 6 | 24.9 | 0.241 | 0.00000121 | 310 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000120 | 0.000120 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000703 | 0.0000703 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000659 | 0.0000653 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Essential subunit of the N-oligosaccharyl transferase (OST) complex which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains. {ECO:0000250|UniProtKB:E2RQ08, ECO:0000250|UniProtKB:Q9GMB0, ECO:0000305}.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);N-Glycan biosynthesis - Homo sapiens (human);Proteasome Degradation;proteasome complex;SRP-dependent cotranslational protein targeting to membrane;Translation;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-Glycan biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.321
Intolerance Scores
- loftool
- 0.101
- rvis_EVS
- -0.02
- rvis_percentile_EVS
- 52.09
Haploinsufficiency Scores
- pHI
- 0.233
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.464
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.867
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rpn1
- Phenotype
Gene ontology
- Biological process
- cellular protein modification process;protein N-linked glycosylation via asparagine
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;rough endoplasmic reticulum;cytosol;oligosaccharyltransferase complex;membrane;integral component of membrane;melanosome
- Molecular function
- RNA binding;dolichyl-diphosphooligosaccharide-protein glycotransferase activity;protein binding