RANBP10

RAN binding protein 10

Basic information

Region (hg38): 16:67723070-67806560

Links

ENSG00000141084 ∙ NCBI:57610 ∙ OMIM:614031 ∙ HGNC:29285 ∙ Uniprot:Q6VN20 ∙ 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 RANBP10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RANBP10 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	2	4
missense			49	1		50
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	49	3	2

Variants in RANBP10

This is a list of pathogenic ClinVar variants found in the RANBP10 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67726555-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-67727413-G-A		not specified	Uncertain significance (Apr 20, 2023)
16-67727786-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-67727792-G-A		not specified	Uncertain significance (Apr 18, 2023)
16-67727851-G-A		not specified	Uncertain significance (Nov 25, 2024)
16-67727867-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-67727878-C-T		not specified	Uncertain significance (Nov 29, 2023)
16-67727893-T-A		not specified	Uncertain significance (Jun 25, 2024)
16-67728418-C-G		not specified	Uncertain significance (Aug 06, 2024)
16-67728511-G-A		not specified	Likely benign (Dec 20, 2023)
16-67729328-T-A		not specified	Uncertain significance (Jun 21, 2022)
16-67729365-G-T		not specified	Uncertain significance (Sep 17, 2021)
16-67729376-G-A		not specified	Uncertain significance (Aug 01, 2024)
16-67729393-C-G			Likely benign (Feb 01, 2023)
16-67729451-G-A		not specified	Likely benign (Oct 17, 2024)
16-67729452-C-T		Marfanoid habitus and intellectual disability	Uncertain significance (-)
16-67729715-C-A		not specified	Uncertain significance (Oct 08, 2024)
16-67729715-C-T		not specified	Uncertain significance (Oct 04, 2024)
16-67729719-G-A		not specified	Uncertain significance (May 17, 2023)
16-67729755-A-G		not specified	Uncertain significance (Aug 15, 2023)
16-67729763-C-T		not specified	Uncertain significance (Jun 10, 2024)
16-67729766-C-T		not specified	Uncertain significance (Oct 17, 2024)
16-67729769-G-A		not specified	Uncertain significance (Nov 02, 2023)
16-67729778-C-T		not specified	Uncertain significance (Mar 15, 2024)
16-67729781-C-T		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RANBP10	protein_coding	protein_coding	ENST00000317506	14	83551

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0314	125685	0	57	125742	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	286	370	0.774	0.0000209	4043
Missense in Polyphen		105	166.11	0.63212		1903
Synonymous	0.261	149	153	0.973	0.00000922	1213
Loss of Function	4.49	5	32.8	0.153	0.00000180	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00154	0.00154
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000357	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as an adapter protein to couple membrane receptors to intracellular signaling pathways (Probable). 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). Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but does not affect estrogen-induced transactivation (PubMed:18222118). Acts as a guanine nucleotide exchange factor (GEF) for RAN GTPase. May play an essential role in hemostasis and in maintaining microtubule dynamics with respect to both platelet shape and function (By similarity). {ECO:0000250|UniProtKB:Q6VN19, ECO:0000269|PubMed:18222118, ECO:0000269|PubMed:29911972, ECO:0000305}.
• Pathway: Signal Transduction;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: 0.113

Intolerance Scores

• loftool: 0.120
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.586
• hipred: Y
• hipred_score: 0.755
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ranbp10
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype

Gene ontology

• Cellular component: ubiquitin ligase complex;nucleus;cytosol
• Molecular function: protein binding