RANBP1

RAN binding protein 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 22:20115937-20127355

Links

ENSG00000099901 ∙ NCBI:5902 ∙ OMIM:601180 ∙ HGNC:9847 ∙ Uniprot:P43487 ∙ 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 RANBP1 gene.

• Inborn genetic diseases (18 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RANBP1 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	1	3
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	18	2	1

Variants in RANBP1

This is a list of pathogenic ClinVar variants found in the RANBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-20116063-C-T		not specified	Uncertain significance (Apr 08, 2022)
22-20116081-G-A		not specified	Uncertain significance (Feb 17, 2023)
22-20116113-A-G		not specified	Uncertain significance (Dec 06, 2022)
22-20116122-A-G		not specified	Uncertain significance (Mar 14, 2023)
22-20116149-G-A		not specified	Uncertain significance (Sep 29, 2022)
22-20116203-C-T		not specified	Uncertain significance (Feb 27, 2024)
22-20116255-C-T		not specified	Uncertain significance (Jan 19, 2022)
22-20116257-C-A		not specified	Uncertain significance (Dec 12, 2022)
22-20116298-A-G			Likely benign (Jul 01, 2022)
22-20116303-C-T		not specified	Uncertain significance (Nov 18, 2022)
22-20116320-A-G		not specified	Uncertain significance (Oct 04, 2022)
22-20116341-T-A		not specified	Uncertain significance (Feb 27, 2024)
22-20116353-C-T		not specified	Uncertain significance (Nov 21, 2022)
22-20116383-C-G		not specified	Uncertain significance (Dec 16, 2023)
22-20116427-A-C			Likely benign (Mar 01, 2022)
22-20116431-G-C		not specified	Uncertain significance (Oct 25, 2023)
22-20116462-G-C		not specified	Uncertain significance (Dec 22, 2023)
22-20116593-C-T		not specified	Uncertain significance (May 17, 2023)
22-20119021-T-A		not specified	Uncertain significance (Dec 17, 2023)
22-20119025-G-T		not specified	Uncertain significance (Aug 06, 2021)
22-20122264-G-C		not specified	Uncertain significance (Jul 12, 2023)
22-20122383-G-A		not specified	Uncertain significance (Jan 06, 2023)
22-20125317-T-C		not specified	Uncertain significance (Nov 09, 2021)
22-20125324-G-T		not specified	Uncertain significance (Jul 12, 2023)
22-20125385-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RANBP1	protein_coding	protein_coding	ENST00000331821	6	11418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.822	0.177	125275	0	1	125276	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	58	119	0.486	0.00000717	1344
Missense in Polyphen		5	38.05	0.1314		424
Synonymous	-1.06	56	46.7	1.20	0.00000326	355
Loss of Function	2.65	1	10.1	0.0993	5.96e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in RAN-dependent nucleocytoplasmic transport. Alleviates the TNPO1-dependent inhibition of RAN GTPase activity and mediates the dissociation of RAN from proteins involved in transport into the nucleus (By similarity). Induces a conformation change in the complex formed by XPO1 and RAN that triggers the release of the nuclear export signal of cargo proteins (PubMed:20485264). Promotes the disassembly of the complex formed by RAN and importin beta. Promotes dissociation of RAN from a complex with KPNA2 and CSE1L (By similarity). Required for normal mitotic spindle assembly and normal progress through mitosis via its effect on RAN (PubMed:17671426). Does not increase the RAN GTPase activity by itself, but increases GTP hydrolysis mediated by RANGAP1 (PubMed:7882974). Inhibits RCC1-dependent exchange of RAN-bound GDP by GTP (PubMed:7882974, PubMed:7616957). {ECO:0000250|UniProtKB:P34022, ECO:0000269|PubMed:17671426, ECO:0000269|PubMed:20485264, ECO:0000269|PubMed:7616957, ECO:0000269|PubMed:7882974}.
• Pathway: HTLV-I infection - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Disease;role of ran in mitotic spindle regulation;cycling of ran in nucleocytoplasmic transport;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;Infectious disease;mechanism of protein import into the nucleus;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.287
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.764
• hipred: Y
• hipred_score: 0.744
• ghis: 0.735

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ranbp1
• Phenotype: growth/size/body region phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: signal transduction;viral process;positive regulation of GTPase activity;positive regulation of mitotic centrosome separation;intracellular transport
• Cellular component: nucleus;nuclear envelope;nuclear pore;cytoplasm;centrosome;cytosol
• Molecular function: GDP-dissociation inhibitor activity;GTPase activator activity;protein binding;Ran GTPase binding;cadherin binding