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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:P04843AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (12 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.

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
2
clinvar
2
missense
13
clinvar
1
clinvar
14
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 13 0 3

Variants in RPN1

This is a list of pathogenic ClinVar variants found in the RPN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
3-128620541-G-A not specified Uncertain significance (Feb 22, 2023)2487273
3-128620588-G-A Benign (Apr 30, 2018)720033
3-128622232-C-G not specified Uncertain significance (Jan 23, 2023)2455412
3-128622303-T-C not specified Uncertain significance (Jun 06, 2023)2530890
3-128625535-T-C Benign (Apr 30, 2018)713300
3-128625538-G-C not specified Uncertain significance (Sep 20, 2023)3156127
3-128625589-T-C not specified Uncertain significance (Dec 19, 2022)2336884
3-128625643-G-A not specified Uncertain significance (Oct 25, 2022)3156126
3-128625917-G-T not specified Uncertain significance (Aug 16, 2022)2307316
3-128625978-G-A not specified Uncertain significance (Mar 17, 2023)2526188
3-128630091-T-C not specified Uncertain significance (Jan 18, 2023)2476481
3-128632025-C-G not specified Uncertain significance (Jul 19, 2023)2612666
3-128632052-T-C not specified Uncertain significance (Feb 28, 2024)3156133
3-128632079-G-A Hereditary breast ovarian cancer syndrome Uncertain significance (Aug 01, 2020)981860
3-128632135-T-G not specified Uncertain significance (Mar 07, 2024)3156132
3-128637793-G-A Benign (Jun 01, 2018)774848
3-128637856-C-T Benign (Apr 30, 2018)709402
3-128637893-C-T not specified Uncertain significance (Jan 23, 2024)2358618
3-128637969-C-T not specified Uncertain significance (Dec 14, 2023)3156131
3-128638096-G-C not specified Uncertain significance (Jan 24, 2024)3156129
3-128644979-T-C not specified Uncertain significance (Oct 04, 2022)2213252
3-128650607-C-T not specified Uncertain significance (Nov 29, 2023)3156128
3-128650748-G-A not specified Uncertain significance (Dec 21, 2022)2349930
3-128650793-G-A not specified Uncertain significance (Oct 12, 2021)2254204

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