RPN2

ribophorin II, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 20:37178410-37241619

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 (138 variants)
not_specified (65 variants)
not_provided (18 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. These statistics are base on transcript: NM_000002951.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	33 clinvar	2 clinvar	38
missense			110 clinvar	10 clinvar	3 clinvar	123
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	114	43	5

Loading clinvar variants...

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