RPN2

ribophorin II, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 20:37178409-37241619

Links

ENSG00000118705 ∙ NCBI:6185 ∙ OMIM:180490 ∙ HGNC:10382 ∙ Uniprot:P04844 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	23	3	27
missense			66	6	3	75
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3	2	6
non coding			1	22	35	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)
20-37178751-A-T			Benign (Sep 05, 2018)
20-37178834-C-T			Benign (Sep 05, 2018)
20-37179358-T-TGGCGCCGCCGGGTGAGGAGTTGCGCGTGG		not specified	Benign (Mar 29, 2016)
20-37179368-G-C		Congenital disorder of glycosylation	Uncertain significance (Dec 31, 2022)
20-37179380-G-T		Congenital disorder of glycosylation	Likely benign (Dec 30, 2021)
20-37179381-C-G		Congenital disorder of glycosylation	Likely benign (Aug 02, 2023)
20-37179387-G-GCTTATAGACGGGGCCCCGCGGCCGGCACT		Congenital disorder of glycosylation	Likely benign (Jan 22, 2024)
20-37179387-G-GCTTATAGACAGGGCCCGCGGCCGGCACT		Congenital disorder of glycosylation	Likely benign (Oct 20, 2022)
20-37179387-G-GCTTATAGACAGGGCCCGGCGGCCGGCACT		Congenital disorder of glycosylation	Likely benign (Apr 26, 2023)
20-37179387-G-GCTTACAGACAGGGCCCCGCGGCCGACACT		Congenital disorder of glycosylation	Likely benign (Nov 14, 2023)
20-37179387-G-GCTTATAGACAGGGCCCCGCGGCCGGCACT		Congenital disorder of glycosylation	Likely benign (Jan 31, 2024)
20-37179387-G-GCTTACAGACAGGGCCCCGCGGCCGGCACT		Congenital disorder of glycosylation	Likely benign (Jan 29, 2024)
20-37179610-C-T			Benign (Jun 20, 2021)
20-37184071-C-T			Likely benign (Jan 23, 2020)
20-37184123-C-A			Benign (Sep 05, 2018)
20-37184171-C-T		Congenital disorder of glycosylation	Likely benign (Nov 08, 2021)
20-37184176-C-G		Congenital disorder of glycosylation	Likely benign (Jan 17, 2024)
20-37184191-G-A		Congenital disorder of glycosylation	Uncertain significance (Jan 15, 2024)
20-37184217-A-G		Congenital disorder of glycosylation	Uncertain significance (May 20, 2022)
20-37184230-G-A		Congenital disorder of glycosylation	Uncertain significance (Dec 30, 2020)
20-37184244-T-A		Congenital disorder of glycosylation	Likely benign (Jun 10, 2023)
20-37184251-C-T		Congenital disorder of glycosylation	Uncertain significance (Dec 05, 2022)
20-37184265-C-T		Congenital disorder of glycosylation	Likely benign (Jul 30, 2020)
20-37184285-C-T		Congenital disorder of glycosylation	Uncertain significance (Aug 19, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPN2	protein_coding	protein_coding	ENST00000237530	17	63210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.115	0.885	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00683	336	336	0.999	0.0000198	4106
Missense in Polyphen		127	147.66	0.86008		1884
Synonymous	0.236	134	138	0.974	0.00000895	1293
Loss of Function	3.87	8	31.4	0.255	0.00000156	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000430	0.000425
Other	0.000328	0.000326

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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