RANBP3

RAN binding protein 3

Basic information

Region (hg38): 19:5916138-5978142

Links

ENSG00000031823 ∙ NCBI:8498 ∙ OMIM:603327 ∙ HGNC:9850 ∙ Uniprot:Q9H6Z4 ∙ 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 RANBP3 gene.

• Inborn genetic diseases (22 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RANBP3 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						0
missense			22		1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	1

Variants in RANBP3

This is a list of pathogenic ClinVar variants found in the RANBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-5917621-C-T		not specified	Uncertain significance (Nov 17, 2023)
19-5917642-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-5918573-C-T		not specified	Uncertain significance (May 01, 2023)
19-5918626-T-C		not specified	Uncertain significance (May 24, 2023)
19-5921206-C-T		not specified	Uncertain significance (Jun 13, 2022)
19-5921227-T-C		not specified	Uncertain significance (Jan 02, 2024)
19-5923259-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-5924882-G-A			Benign (May 21, 2018)
19-5924885-C-T		not specified	Uncertain significance (Sep 29, 2022)
19-5925668-C-T		not specified	Uncertain significance (Feb 21, 2024)
19-5925683-C-T		not specified	Uncertain significance (Nov 13, 2023)
19-5925692-G-A		not specified	Uncertain significance (Aug 04, 2021)
19-5925722-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-5932457-T-G		not specified	Uncertain significance (Dec 06, 2022)
19-5932512-G-A		not specified	Uncertain significance (Dec 14, 2022)
19-5933417-C-T		not specified	Uncertain significance (Jun 05, 2023)
19-5933458-C-T		not specified	Uncertain significance (Aug 15, 2023)
19-5941823-C-T		not specified	Uncertain significance (Jun 16, 2023)
19-5951398-C-T		not specified	Uncertain significance (May 27, 2022)
19-5951409-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-5951448-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-5951458-C-G		not specified	Uncertain significance (Jun 28, 2023)
19-5951517-C-T		not specified	Uncertain significance (Jul 11, 2023)
19-5951520-G-A		not specified	Uncertain significance (Aug 19, 2023)
19-5951523-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RANBP3	protein_coding	protein_coding	ENST00000340578	17	62004

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000311	122341	0	1	122342	0.00000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	258	356	0.724	0.0000221	3679
Missense in Polyphen		74	129.73	0.5704		1325
Synonymous	-0.626	170	160	1.06	0.0000121	1118
Loss of Function	5.22	1	33.7	0.0297	0.00000169	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000913	0.00000913
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a cofactor for XPO1/CRM1-mediated nuclear export, perhaps as export complex scaffolding protein. Bound to XPO1/CRM1, stabilizes the XPO1/CRM1-cargo interaction. In the absence of Ran-bound GTP prevents binding of XPO1/CRM1 to the nuclear pore complex. Binds to CHC1/RCC1 and increases the guanine nucleotide exchange activity of CHC1/RCC1. Recruits XPO1/CRM1 to CHC1/RCC1 in a Ran-dependent manner. Negative regulator of TGF- beta signaling through interaction with the R-SMAD proteins, SMAD2 and SMAD3, and mediating their nuclear export. {ECO:0000269|PubMed:11425870, ECO:0000269|PubMed:11571268, ECO:0000269|PubMed:11932251, ECO:0000269|PubMed:19289081, ECO:0000269|PubMed:9637251}.
• Pathway: HTLV-I infection - Homo sapiens (human);WNT-Ncore;Canonical Wnt signaling pathway (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.0273
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.08

Haploinsufficiency Scores

• pHI: 0.652
• hipred: Y
• hipred_score: 0.735
• ghis: 0.655

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ranbp3

Gene ontology

• Biological process: protein export from nucleus;positive regulation of GTPase activity
• Cellular component: nucleus;nuclear pore;nucleoplasm;cytoplasm
• Molecular function: GTPase activator activity;protein binding;Ran GTPase binding;R-SMAD binding