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GeneBe

RPN2

ribophorin II, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 20:37178409-37241619

Links

ENSG00000118705NCBI:6185OMIM:180490HGNC:10382Uniprot:P04844AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPN2 gene.

  • Congenital disorder of glycosylation (111 variants)
  • not provided (42 variants)
  • Inborn genetic diseases (24 variants)
  • not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPN2 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
1
clinvar
23
clinvar
3
clinvar
27
missense
66
clinvar
6
clinvar
3
clinvar
75
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
1
clinvar
22
clinvar
35
clinvar
58
Total 0 0 69 51 41

Variants in RPN2

This is a list of pathogenic ClinVar variants found in the RPN2 region.

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

Position Type Phenotype Significance ClinVar
20-37178722-C-A Benign (Sep 05, 2018)1238363
20-37178751-A-T Benign (Sep 05, 2018)1249784
20-37178834-C-T Benign (Sep 05, 2018)1253465
20-37179358-T-TGGCGCCGCCGGGTGAGGAGTTGCGCGTGG not specified Benign (Mar 29, 2016)403105
20-37179368-G-C Congenital disorder of glycosylation Uncertain significance (Dec 31, 2022)2771311
20-37179380-G-T Congenital disorder of glycosylation Likely benign (Dec 30, 2021)1909002
20-37179387-G-GCTTATAGACGGGGCCCCGCGGCCGGCACT Congenital disorder of glycosylation Likely benign (Sep 08, 2022)2041031
20-37179387-G-GCTTATAGACAGGGCCCGCGGCCGGCACT Congenital disorder of glycosylation Likely benign (Oct 20, 2022)2159331
20-37179387-G-GCTTATAGACAGGGCCCGGCGGCCGGCACT Congenital disorder of glycosylation Likely benign (Aug 23, 2022)2120293
20-37179387-G-GCTTACAGACAGGGCCCCGCGGCCGACACT Congenital disorder of glycosylation Likely benign (Jun 28, 2022)1986160
20-37179387-G-GCTTATAGACAGGGCCCCGCGGCCGGCACT Congenital disorder of glycosylation Likely benign (Nov 01, 2022)1115482
20-37179387-G-GCTTACAGACAGGGCCCCGCGGCCGGCACT Congenital disorder of glycosylation Likely benign (Oct 22, 2022)1148510
20-37179610-C-T Benign (Jun 20, 2021)1272265
20-37184071-C-T Likely benign (Jan 23, 2020)1318003
20-37184123-C-A Benign (Sep 05, 2018)1275370
20-37184171-C-T Congenital disorder of glycosylation Likely benign (Nov 08, 2021)763560
20-37184191-G-A Congenital disorder of glycosylation Uncertain significance (Jan 15, 2024)2193956
20-37184217-A-G Congenital disorder of glycosylation Uncertain significance (May 20, 2022)2122575
20-37184230-G-A Congenital disorder of glycosylation Uncertain significance (Sep 02, 2021)1401248
20-37184251-C-T Congenital disorder of glycosylation Uncertain significance (Dec 05, 2022)2051509
20-37184265-C-T Congenital disorder of glycosylation Likely benign (Jul 30, 2020)1148227
20-37184285-C-T Congenital disorder of glycosylation Uncertain significance (Aug 24, 2021)1022440
20-37184323-T-C Congenital disorder of glycosylation Uncertain significance (Jul 12, 2022)843831
20-37184351-G-C Congenital disorder of glycosylation Uncertain significance (Jul 27, 2023)2746907
20-37184354-C-T Congenital disorder of glycosylation • Inborn genetic diseases Conflicting classifications of pathogenicity (Aug 09, 2022)572778

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPN2protein_codingprotein_codingENST00000237530 1763210
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1150.8851257230251257480.0000994
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.006833363360.9990.00001984106
Missense in Polyphen127147.660.860081884
Synonymous0.2361341380.9740.000008951293
Loss of Function3.87831.40.2550.00000156371

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00007060.0000703
Middle Eastern0.00005440.0000544
South Asian0.0004300.000425
Other0.0003280.000326

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:F1PCT7, 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
0.472

Intolerance Scores

loftool
0.722
rvis_EVS
-0.35
rvis_percentile_EVS
29.49

Haploinsufficiency Scores

pHI
0.346
hipred
Y
hipred_score
0.666
ghis
0.568

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.848

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpn2
Phenotype
homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name
rpn2
Affected structure
mandibular arch skeleton
Phenotype tag
abnormal
Phenotype quality
decreased length

Gene ontology

Biological process
cellular protein modification process;protein N-linked glycosylation;aging;protein N-linked glycosylation via asparagine;response to drug
Cellular component
autophagosome membrane;endoplasmic reticulum membrane;rough endoplasmic reticulum;oligosaccharyltransferase complex;membrane;integral component of membrane
Molecular function
dolichyl-diphosphooligosaccharide-protein glycotransferase activity;protein binding;ribosome binding