GeneBe

SBF2

SET binding factor 2, the group of DENN domain containing|Myotubularins|Pleckstrin homology domain containing

Basic information

Region (hg38): 11:9776776-10304877

Previous symbols: [ "CMT4B2" ]

Links

ENSG00000133812 ∙ NCBI:81846 ∙ OMIM:607697 ∙ HGNC:2135 ∙ Uniprot:Q86WG5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Charcot-Marie-Tooth disease type 4B2 (Supportive), mode of inheritance: AR
  • Charcot-Marie-Tooth disease type 4B2 (Strong), mode of inheritance: AR
  • Charcot-Marie-Tooth disease type 4B2 (Definitive), mode of inheritance: AR
  • Charcot-Marie-Tooth disease type 4B2 (Strong), mode of inheritance: AR
  • Charcot-Marie-Tooth disease type 4B2 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Charcot-Marie-Tooth disease, type 4B2AROphthalmologic; PharmacogenomicOpen-angle glaucoma is typically asymptomatic until late stages, when irreversible nerve damage has already taken place; As the condition may include early-onset hearing loss, intervention related to speech and language development may be beneficial; Agents that may contribute to glaucoma should be avoidedAudiologic/Otolaryngologic; Neurologic; Ophthalmologic9521281; 10932274; 12687498; 12554688; 15477569; 15304601; 23334996
Several families with CMT4B2 with early-onset glaucoma have been reported; One report has also described homozygous variants associated with Congenital thrombocytopenia, autosomal recessive

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SBF2 gene.

  • Charcot-Marie-Tooth_disease_type_4 (1298 variants)
  • Inborn_genetic_diseases (335 variants)
  • not_provided (269 variants)
  • Charcot-Marie-Tooth_disease_type_4B2 (156 variants)
  • Charcot-Marie-Tooth_disease (108 variants)
  • not_specified (105 variants)
  • SBF2-related_disorder (30 variants)
  • Tip-toe_gait (7 variants)
  • Peripheral_neuropathy (1 variants)
  • Congenital_thrombocytopenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030962.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
364
clinvar
2
clinvar
 373
missense
1
clinvar
4
clinvar
748
clinvar
11
clinvar
1
clinvar
 765
nonsense
27
clinvar
4
clinvar
2
clinvar
 33
start loss
0
frameshift
15
clinvar
8
clinvar
4
clinvar
 27
splice donor/acceptor (+/-2bp)
5
clinvar
21
clinvar
3
clinvar
 29
Total 48 37 764 375 3

Highest pathogenic variant AF is 0.000016211497

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SBF2protein_codingprotein_codingENST00000256190 40515541
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
6.38e-101.001256820661257480.000262
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.198499520.8910.000050712151
Missense in Polyphen197298.430.660133792
Synonymous-0.8703623421.060.00001793533
Loss of Function5.983599.30.3530.000005231209

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006620.000662
Ashkenazi Jewish0.0002980.000298
East Asian0.0001090.000109
Finnish0.00004640.0000462
European (Non-Finnish)0.0002820.000281
Middle Eastern0.0001090.000109
South Asian0.0003600.000359
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB28. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. {ECO:0000269|PubMed:20937701}.;
Pathway
Vesicle-mediated transport;Membrane Trafficking;Metabolism of lipids;Metabolism;Rab regulation of trafficking;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

pRec
0.169

Intolerance Scores

loftool
0.0995
rvis_EVS
-2
rvis_percentile_EVS
1.73

Haploinsufficiency Scores

pHI
0.0582
hipred
N
hipred_score
0.426
ghis
0.607

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.874

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sbf2
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process
myelination;regulation of GTPase activity;protein tetramerization
Cellular component
vacuolar membrane;cytosol;membrane
Molecular function
protein binding;Rab guanyl-nucleotide exchange factor activity;phosphatase regulator activity;phosphatase binding;phosphatidylinositol binding;protein homodimerization activity