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GeneBe

RPN1

ribophorin I, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 3:128619968-128681075

Links

ENSG00000163902NCBI:6184OMIM:180470HGNC:10381Uniprot:P04843AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPN1 gene.

  • 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)link
3-128620588-G-A Benign (Apr 30, 2018)link
3-128622232-C-G Inborn genetic diseases Uncertain significance (Jan 23, 2023)link
3-128622303-T-C Inborn genetic diseases Uncertain significance (Jun 06, 2023)link
3-128625535-T-C Benign (Apr 30, 2018)link
3-128625589-T-C Inborn genetic diseases Uncertain significance (Dec 19, 2022)link
3-128625917-G-T Inborn genetic diseases Uncertain significance (Aug 16, 2022)link
3-128625978-G-A Inborn genetic diseases Uncertain significance (Mar 17, 2023)link
3-128630091-T-C Inborn genetic diseases Uncertain significance (Jan 18, 2023)link
3-128632025-C-G Inborn genetic diseases Uncertain significance (Jul 19, 2023)link
3-128632079-G-A Hereditary breast ovarian cancer syndrome Uncertain significance (Aug 01, 2020)link
3-128637793-G-A Benign (Jun 01, 2018)link
3-128637856-C-T Benign (Apr 30, 2018)link
3-128637893-C-T Inborn genetic diseases Uncertain significance (Nov 09, 2021)link
3-128644979-T-C Inborn genetic diseases Uncertain significance (Oct 04, 2022)link
3-128650748-G-A Inborn genetic diseases Uncertain significance (Dec 21, 2022)link
3-128650793-G-A Inborn genetic diseases Uncertain significance (Oct 12, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPN1protein_codingprotein_codingENST00000296255 1061102
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2390.7611257330151257480.0000596
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7363053430.8880.00001883939
Missense in Polyphen80103.910.769861243
Synonymous-0.07721411401.010.000007501243
Loss of Function3.51624.90.2410.00000121310

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001200.000120
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00007030.0000703
Middle Eastern0.000.00
South Asian0.00006590.0000653
Other0.0001640.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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