RANBP9

RAN binding protein 9, the group of CTLH complex

Basic information

Region (hg38): 6:13621498-13711835

Links

ENSG00000010017 ∙ NCBI:10048 ∙ OMIM:603854 ∙ HGNC:13727 ∙ Uniprot:Q96S59 ∙ 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 RANBP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RANBP9 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				1		1
missense			42			42
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	42	1	0

Variants in RANBP9

This is a list of pathogenic ClinVar variants found in the RANBP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-13622372-T-C		not specified	Uncertain significance (Aug 16, 2021)
6-13622397-A-C		not specified	Uncertain significance (Jan 24, 2024)
6-13622414-C-T		not specified	Uncertain significance (May 27, 2022)
6-13625691-C-T		not specified	Uncertain significance (Dec 22, 2023)
6-13632397-C-G		not specified	Uncertain significance (Jul 05, 2023)
6-13632434-T-C		not specified	Uncertain significance (Jul 16, 2021)
6-13632453-G-T		not specified	Uncertain significance (May 23, 2023)
6-13632490-C-A		not specified	Uncertain significance (Jun 16, 2024)
6-13634448-T-G		not specified	Uncertain significance (May 25, 2022)
6-13634458-C-T		not specified	Uncertain significance (Sep 26, 2023)
6-13634545-C-T		not specified	Uncertain significance (Nov 07, 2023)
6-13637877-G-C		not specified	Uncertain significance (Jun 18, 2021)
6-13639595-G-A		not specified	Uncertain significance (Aug 13, 2021)
6-13639652-C-T		not specified	Uncertain significance (Oct 12, 2021)
6-13639748-C-T		not specified	Uncertain significance (Jan 09, 2024)
6-13644550-T-C		not specified	Uncertain significance (May 08, 2024)
6-13644641-T-C		not specified	Uncertain significance (Dec 19, 2023)
6-13644663-G-A		not specified	Uncertain significance (Apr 07, 2023)
6-13652689-G-A			Likely benign (Nov 17, 2017)
6-13657117-T-C		not specified	Uncertain significance (Jun 10, 2022)
6-13710974-T-C		not specified	Uncertain significance (Apr 01, 2024)
6-13711009-G-A		not specified	Uncertain significance (May 30, 2024)
6-13711027-T-G		not specified	Uncertain significance (Jul 09, 2021)
6-13711106-G-A		not specified	Uncertain significance (Mar 01, 2023)
6-13711110-G-C			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RANBP9	protein_coding	protein_coding	ENST00000011619	14	90067

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000108	118838	0	1	118839	0.00000421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	258	335	0.771	0.0000165	4683
Missense in Polyphen		103	169.01	0.60941		1989
Synonymous	-1.63	144	121	1.19	0.00000639	1451
Loss of Function	5.45	1	36.5	0.0274	0.00000209	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000566	0.0000566
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000566	0.0000566
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as scaffolding protein, and as adapter protein to couple membrane receptors to intracellular signaling pathways (Probable). Acts as a mediator of cell spreading and actin cytoskeleton rearrangement (PubMed:18710924). Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 (PubMed:29911972). May be involved in signaling of ITGB2/LFA- 1 and other integrins (PubMed:14722085). Enhances HGF-MET signaling by recruiting Sos and activating the Ras pathway (PubMed:12147692). Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but not affect estrogen-induced transactivation (PubMed:12361945, PubMed:18222118). Stabilizes TP73 isoform Alpha, probably by inhibiting its ubiquitination, and increases its proapoptotic activity (PubMed:15558019). Inhibits the kinase activity of DYRK1A and DYRK1B. Inhibits FMR1 binding to RNA. {ECO:0000269|PubMed:12147692, ECO:0000269|PubMed:12361945, ECO:0000269|PubMed:14500717, ECO:0000269|PubMed:14722085, ECO:0000269|PubMed:15381419, ECO:0000269|PubMed:15558019, ECO:0000269|PubMed:18222118, ECO:0000269|PubMed:18710924, ECO:0000269|PubMed:29911972, ECO:0000305}.
• Pathway: Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Developmental Biology;Signal Transduction;AndrogenReceptor;BDNF;Coregulation of Androgen receptor activity;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;L1CAM interactions;Axon guidance;MET activates RAS signaling;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met) (Consensus)

Recessive Scores

• pRec: 0.206

Intolerance Scores

• loftool: 0.0392
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.771
• hipred: Y
• hipred_score: 0.825
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.806

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ranbp9
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ranbp9
• Affected structure: Muller cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: MAPK cascade;microtubule nucleation;axon guidance;protein-containing complex assembly;negative regulation of ERK1 and ERK2 cascade
• Cellular component: ubiquitin ligase complex;nucleus;cytoplasm;cytosol;microtubule associated complex;plasma membrane
• Molecular function: Ras guanyl-nucleotide exchange factor activity;protein binding;Ran GTPase binding;enzyme binding