RANBP3L

RAN binding protein 3 like

Basic information

Region (hg38): 5:36246913-36302114

Links

ENSG00000164188 ∙ NCBI:202151 ∙ OMIM:616391 ∙ HGNC:26353 ∙ Uniprot:Q86VV4 ∙ 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 RANBP3L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RANBP3L 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	26	1	1

Variants in RANBP3L

This is a list of pathogenic ClinVar variants found in the RANBP3L region.

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

Position	Type	Phenotype	Significance	ClinVar
5-36248650-T-G			Benign (Jan 17, 2024)
5-36249670-G-A		not specified	Uncertain significance (Jul 14, 2023)
5-36251353-C-G		not specified	Uncertain significance (Dec 31, 2023)
5-36251411-T-C		not specified	Uncertain significance (Jan 03, 2024)
5-36251430-T-C		not specified	Likely benign (Aug 15, 2024)
5-36253673-A-G		not specified	Uncertain significance (Aug 12, 2021)
5-36253681-A-G		not specified	Uncertain significance (Oct 12, 2021)
5-36253717-G-T		not specified	Uncertain significance (Dec 17, 2023)
5-36253780-T-C		not specified	Uncertain significance (Jul 25, 2023)
5-36255491-C-T		not specified	Uncertain significance (Mar 11, 2022)
5-36255499-G-A		not specified	Uncertain significance (Dec 28, 2023)
5-36255526-G-A		not specified	Uncertain significance (Jun 27, 2022)
5-36256984-A-G		not specified	Uncertain significance (Mar 07, 2024)
5-36256999-C-T		not specified	Uncertain significance (Oct 30, 2023)
5-36257519-T-A		not specified	Uncertain significance (Mar 29, 2023)
5-36260830-T-C		not specified	Uncertain significance (Dec 02, 2022)
5-36260848-C-T		not specified	Uncertain significance (Feb 27, 2024)
5-36260854-T-C		not specified	Uncertain significance (Aug 28, 2024)
5-36261966-T-C		not specified	Uncertain significance (Dec 28, 2023)
5-36261985-C-T		not specified	Uncertain significance (Apr 22, 2022)
5-36262036-C-T		not specified	Uncertain significance (Sep 27, 2024)
5-36262038-G-A		not specified	Uncertain significance (Oct 06, 2023)
5-36264963-T-C		not specified	Uncertain significance (Sep 27, 2024)
5-36264976-C-T		not specified	Uncertain significance (Nov 15, 2024)
5-36269437-C-T		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RANBP3L	protein_coding	protein_coding	ENST00000502994	15	53681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.80e-16	0.0610	125678	1	68	125747	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.426	224	243	0.923	0.0000119	3196
Missense in Polyphen		56	61.377	0.91239		841
Synonymous	0.588	78	84.9	0.919	0.00000400	891
Loss of Function	0.780	26	30.7	0.848	0.00000165	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000280	0.000280
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.000219	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000219	0.000217
South Asian	0.00128	0.00124
Other	0.000175	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nuclear export factor for BMP-specific SMAD1/5/8 that plays a critical role in terminating BMP signaling and regulating mesenchymal stem cell differentiation by blocking osteoblast differentiation to promote myogenic differention. Directly recognizes dephosphorylated SMAD1/5/8 and mediates their nuclear export in a Ran-dependent manner. {ECO:0000250|UniProtKB:Q6PDH4, ECO:0000269|PubMed:25755279}.

Intolerance Scores

• loftool: 0.988
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.123
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ranbp3l

Gene ontology

• Biological process: protein export from nucleus;positive regulation of GTPase activity;positive regulation of myoblast differentiation;negative regulation of osteoblast differentiation;mesenchymal cell differentiation involved in bone development
• Cellular component: nucleus;nuclear pore;cytoplasm
• Molecular function: GTPase activator activity;Ran GTPase binding;SMAD binding