RPN1

ribophorin I, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 3:128619969-128681075

Links

ENSG00000163902 ∙ NCBI:6184 ∙ OMIM:180470 ∙ HGNC:10381 ∙ Uniprot:P04843 ∙ 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 RPN1 gene.

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	2
missense			32	2	1	35
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	32	2	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
3-128620505-A-G		not specified	Uncertain significance (Jun 04, 2024)
3-128620541-G-A		not specified	Uncertain significance (Feb 22, 2023)
3-128620588-G-A			Benign (Apr 30, 2018)
3-128622232-C-G		not specified	Uncertain significance (Feb 18, 2025)
3-128622262-C-T		not specified	Uncertain significance (Jan 27, 2025)
3-128622303-T-C		not specified	Uncertain significance (Jun 06, 2023)
3-128622354-G-C		not specified	Uncertain significance (Nov 14, 2024)
3-128625535-T-C			Benign (Apr 30, 2018)
3-128625538-G-C		not specified	Uncertain significance (Sep 20, 2023)
3-128625557-G-A		not specified	Uncertain significance (May 08, 2024)
3-128625589-T-C		not specified	Uncertain significance (Dec 19, 2022)
3-128625643-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-128625917-G-T		not specified	Uncertain significance (Aug 16, 2022)
3-128625933-G-A		not specified	Uncertain significance (Dec 23, 2024)
3-128625978-G-A		not specified	Uncertain significance (Mar 17, 2023)
3-128630091-T-C		not specified	Uncertain significance (Jan 18, 2023)
3-128631955-G-A		not specified	Uncertain significance (Jul 17, 2024)
3-128631964-G-C		not specified	Uncertain significance (Jul 17, 2024)
3-128632025-C-A		not specified	Uncertain significance (Jul 09, 2024)
3-128632025-C-G		not specified	Uncertain significance (Jul 19, 2023)
3-128632027-G-A		not specified	Uncertain significance (Feb 11, 2025)
3-128632052-T-C		not specified	Uncertain significance (Feb 28, 2024)
3-128632079-G-A		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
3-128632132-T-C		not specified	Uncertain significance (Jun 07, 2024)
3-128632135-T-G		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPN1	protein_coding	protein_coding	ENST00000296255	10	61102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.239	0.761	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	305	343	0.888	0.0000188	3939
Missense in Polyphen		80	103.91	0.76986		1243
Synonymous	-0.0772	141	140	1.01	0.00000750	1243
Loss of Function	3.51	6	24.9	0.241	0.00000121	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000703	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000659	0.0000653
Other	0.000164	0.000163

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

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

Mouse Genome Informatics

• Gene name: Rpn1

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