RPN1

ribophorin I, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 3:128619968-128681075

Links

ENSG00000163902 ∙ NCBI:6184 ∙ OMIM:180470 ∙ HGNC:10381 ∙ Uniprot:P04843 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

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 (6 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant					1	1
non coding						0
Total	0	0	7	0	4

Variants in RPN1

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

Position	Type	Phenotype	Significance	ClinVar
3-128620541-G-A		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
3-128620588-G-A			Benign (Apr 30, 2018)
3-128622232-C-G		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
3-128622303-T-C		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
3-128625535-T-C			Benign (Apr 30, 2018)
3-128625589-T-C		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
3-128625917-G-T		Inborn genetic diseases	Uncertain significance (Aug 16, 2022)
3-128625978-G-A		Inborn genetic diseases	Uncertain significance (Mar 17, 2023)
3-128630091-T-C		Inborn genetic diseases	Uncertain significance (Jan 18, 2023)
3-128632025-C-G		Inborn genetic diseases	Uncertain significance (Jul 19, 2023)
3-128632079-G-A		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
3-128637793-G-A			Benign (Jun 01, 2018)
3-128637856-C-T			Benign (Apr 30, 2018)
3-128637893-C-T		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
3-128644979-T-C		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
3-128650748-G-A		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
3-128650793-G-A		Inborn genetic diseases	Uncertain significance (Oct 12, 2021)

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