RANBP10

protein-coding

RAN binding protein 10

Gene summary

RAN is a small GTPase involved in the assembly of microtubules to form mitotic spindles. The protein encoded by this gene is a cytoplasmic guanine nucleotide exchange factor (GEF) that binds beta-tubulin and has GEF activity toward RAN. The encoded protein plays a role in the formation of noncentrosomal microtubules. In addition, this protein may be involved in the regulation of D(1) receptor signaling by protein kinase C delta and protein kinase C gamma. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

MANE transcript

NM_020850.3

Inheritance

—

ClinVar variants

U:86B:7

Top phenotype

Marfanoid habitus and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr16:67,723,070-67,806,560

External References & Databases

Ensembl (ENSG00000141084)

Transcript & Mutation Effects

hg38 • Region Span ~83.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RANBP10 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 4

Marfanoid habitus and intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020850.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar	2 clinvar	9
missense			79 clinvar	2 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	86	5	2	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020850.3	RefSeq	NP_065901.1	14	MANE Select
ENST00000317506.8	Ensembl	ENSP00000316589.3	14	MANE Select
NM_001320238.2	RefSeq	NP_001307167.1	12	Standard
NM_001320239.2	RefSeq	NP_001307168.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
MET activates RAS signaling
Signaling by MET
Signaling by Receptor Tyrosine Kinases
Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met)

Molecular Function

protein binding

Cellular Component

ubiquitin ligase complex
nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317506
Coding exons: 14
Length: 83551
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125742
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.55	286	370	0.774	0.0000209	4043
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.0015	0.0015	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.120
RVIS EVS: -0.84
RVIS percentile EVS: 11.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.976

Gene Damage Prediction

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