RANBP1

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

Basic information

Region (hg38): 22:20115938-20127355

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.

not_specified (36 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. These statistics are base on transcript: NM_001278639.2. 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			1 clinvar	2 clinvar	1 clinvar	4
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	29	2	1

Loading clinvar variants...

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