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GeneBe

SBF1

SET binding factor 1, the group of Myotubularins|Pleckstrin homology domain containing|DENN domain containing

Basic information

Region (hg38): 22:50443218-50483923

Links

ENSG00000100241NCBI:6305OMIM:603560HGNC:10542Uniprot:O95248AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Charcot-Marie-Tooth disease type 4B3 (Supportive), mode of inheritance: AR
  • Charcot-Marie-Tooth disease type 4B3 (Limited), mode of inheritance: AR
  • Charcot-Marie-Tooth disease type 4B3 (Moderate), mode of inheritance: AR
  • Charcot-Marie-Tooth disease type 4B3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Charcot-Marie-Tooth disease, type 4B3ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic21210780; 23749797; 24799518

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SBF1 gene.

  • not provided (1442 variants)
  • Inborn genetic diseases (107 variants)
  • Charcot-Marie-Tooth disease type 4B3 (98 variants)
  • not specified (19 variants)
  • SBF1-related condition (6 variants)
  • Tip-toe gait (4 variants)
  • Charcot-Marie-Tooth disease X-linked dominant 1 (1 variants)
  • Charcot-Marie-Tooth disease type 4 (1 variants)
  • Microcephaly (1 variants)
  • Peripheral neuropathy (1 variants)
  • Autism spectrum disorder (1 variants)
  • See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBF1 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
8
clinvar
368
clinvar
25
clinvar
401
missense
1
clinvar
590
clinvar
10
clinvar
2
clinvar
603
nonsense
4
clinvar
4
clinvar
1
clinvar
9
start loss
0
frameshift
4
clinvar
2
clinvar
4
clinvar
10
inframe indel
10
clinvar
10
splice donor/acceptor (+/-2bp)
5
clinvar
5
splice region
42
63
6
111
non coding
9
clinvar
249
clinvar
64
clinvar
322
Total 9 11 622 627 91

Highest pathogenic variant AF is 0.0000394

Variants in SBF1

This is a list of pathogenic ClinVar variants found in the SBF1 region.

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

Position Type Phenotype Significance ClinVar
22-50443885-C-T Inborn genetic diseases Uncertain significance (Jul 11, 2023)2598000
22-50443886-G-A Inborn genetic diseases Uncertain significance (Mar 28, 2023)2535360
22-50443888-C-A Inborn genetic diseases Uncertain significance (Dec 06, 2021)2221305
22-50443910-C-T Inborn genetic diseases Uncertain significance (Jul 25, 2023)2595571
22-50443999-G-A Inborn genetic diseases Uncertain significance (Apr 12, 2022)2392117
22-50444074-G-A Inborn genetic diseases Uncertain significance (Jul 13, 2021)2386731
22-50444206-G-C Inborn genetic diseases Uncertain significance (Dec 05, 2022)2332820
22-50444214-G-A Inborn genetic diseases Likely benign (Sep 13, 2023)2593805
22-50446979-C-CGGGCG Likely benign (Sep 20, 2019)1218491
22-50447030-G-A Likely benign (Sep 21, 2018)1193044
22-50447066-A-G Likely benign (Jul 31, 2018)1219790
22-50447148-G-A Likely benign (Dec 29, 2023)728333
22-50447150-CCGACAGGCAG-C Uncertain significance (Mar 11, 2022)2108952
22-50447151-C-T Likely benign (Dec 20, 2023)739996
22-50447152-G-A Uncertain significance (Sep 13, 2022)1426884
22-50447160-G-A Likely benign (Jun 21, 2023)2966126
22-50447170-C-T Inborn genetic diseases Conflicting classifications of pathogenicity (Apr 07, 2023)2192305
22-50447171-G-A Uncertain significance (May 30, 2022)1899753
22-50447187-G-C Likely benign (Sep 04, 2022)2028977
22-50447190-C-T Likely benign (Jan 25, 2024)2177010
22-50447191-G-A Uncertain significance (Jun 19, 2022)1401406
22-50447194-G-A SBF1-related condition Likely benign (Jan 27, 2024)707840
22-50447195-G-A Uncertain significance (Oct 03, 2023)2087170
22-50447197-A-G Uncertain significance (Apr 08, 2022)1981173
22-50447198-C-T Uncertain significance (Sep 24, 2021)1503062

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SBF1protein_codingprotein_codingENST00000380817 4130026
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9990.0006701248630291248920.000116
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.52711791.23e+30.9580.000089312063
Missense in Polyphen422528.320.798765142
Synonymous-7.017405341.390.00003913934
Loss of Function7.321691.60.1750.000004511002

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005820.0000582
Ashkenazi Jewish0.000.00
East Asian0.0001670.000167
Finnish0.00009370.0000928
European (Non-Finnish)0.0001610.000159
Middle Eastern0.0001670.000167
South Asian0.00006560.0000654
Other0.0003350.000329

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probable pseudophosphatase. Lacks several amino acids in the catalytic pocket which renders it catalytically inactive as a phosphatase. The pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases. Inhibits myoblast differentiation in vitro and induces oncogenic transformation in fibroblasts. According to PubMed:20937701, may function as a guanine nucleotide exchange factor (GEF) activating RAB28. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. {ECO:0000269|PubMed:20937701, ECO:0000269|PubMed:9537414}.;
Disease
DISEASE: Charcot-Marie-Tooth disease 4B3 (CMT4B3) [MIM:615284]: A recessive demyelinating form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot- Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Demyelinating neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. By convention autosomal recessive forms of demyelinating Charcot-Marie-Tooth disease are designated CMT4. {ECO:0000269|PubMed:23749797}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Vesicle-mediated transport;Membrane Trafficking;Metabolism of lipids;Metabolism;Synthesis of PIPs at the ER membrane;Rab regulation of trafficking;PI Metabolism;Phospholipid metabolism;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

pRec
0.145

Intolerance Scores

loftool
0.0648
rvis_EVS
-4.05
rvis_percentile_EVS
0.17

Haploinsufficiency Scores

pHI
0.154
hipred
N
hipred_score
0.476
ghis
0.621

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.323

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sbf1
Phenotype
cellular phenotype; endocrine/exocrine gland phenotype; reproductive system 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);

Gene ontology

Biological process
protein dephosphorylation;phosphatidylinositol biosynthetic process;spermatogenesis;regulation of GTPase activity
Cellular component
cytoplasm;endoplasmic reticulum membrane;cytosol;integral component of membrane;nuclear body
Molecular function
protein tyrosine/serine/threonine phosphatase activity;phosphatase activity;Rab guanyl-nucleotide exchange factor activity;phosphatase regulator activity