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SF3B2

splicing factor 3b subunit 2, the group of Armadillo like helical domain containing|SF3b complex

Basic information

Region (hg38): 11:66050728-66069308

Links

ENSG00000087365NCBI:10992OMIM:605591HGNC:10769Uniprot:Q13435AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Craniofacial microsomia 1ADCardiovascularIndividuals have been described with congenital structural cardiovascular anomalies, and surveillance may allow early identification and managementCardiovascular; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic34344887

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SF3B2 gene.

  • Inborn genetic diseases (19 variants)
  • not provided (9 variants)
  • SF3B2-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3B2 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
1
clinvar
1
clinvar
2
missense
22
clinvar
3
clinvar
25
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
0
Total 0 0 23 4 1

Variants in SF3B2

This is a list of pathogenic ClinVar variants found in the SF3B2 region.

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

Position Type Phenotype Significance ClinVar
11-66052385-A-T Hemifacial microsomia Pathogenic (Jul 13, 2023)1342663
11-66052460-G-T Benign/Likely benign (Feb 01, 2023)770770
11-66053037-T-G Inborn genetic diseases Uncertain significance (Jun 24, 2022)2297487
11-66055118-C-G Inborn genetic diseases Uncertain significance (Aug 04, 2023)2616325
11-66055135-G-C Likely benign (Jul 01, 2023)2578660
11-66055140-C-G Inborn genetic diseases Uncertain significance (Aug 02, 2022)2393965
11-66055218-G-C Uncertain significance (Mar 14, 2022)1706330
11-66055269-A-G Inborn genetic diseases Uncertain significance (Jul 26, 2022)2406198
11-66055572-A-G Inborn genetic diseases Uncertain significance (Apr 04, 2023)2532329
11-66055571-G-GAGC Uncertain significance (Jan 01, 2024)3026360
11-66056919-G-C Inborn genetic diseases Uncertain significance (Mar 27, 2023)2530019
11-66057301-A-G Inborn genetic diseases Likely benign (Jan 31, 2024)3160820
11-66057322-C-T Inborn genetic diseases Uncertain significance (Jan 29, 2024)3160821
11-66057328-C-G Inborn genetic diseases Likely benign (Dec 13, 2023)3160822
11-66057331-C-T Inborn genetic diseases Uncertain significance (Nov 03, 2023)3160823
11-66057350-C-T Inborn genetic diseases Uncertain significance (Jul 15, 2021)2355356
11-66057366-G-T SF3B2-related condition Uncertain significance (Jul 18, 2023)2632262
11-66058124-G-T Inborn genetic diseases Uncertain significance (Dec 14, 2021)2266989
11-66058344-C-T Inborn genetic diseases Likely benign (Feb 28, 2023)2469470
11-66058836-C-T Inborn genetic diseases Uncertain significance (Sep 26, 2023)3160824
11-66058911-C-T Inborn genetic diseases Uncertain significance (Aug 28, 2023)2593761
11-66058912-G-A Inborn genetic diseases Likely benign (Mar 06, 2023)2494551
11-66058930-G-A Inborn genetic diseases Uncertain significance (Jan 23, 2024)3160813
11-66058939-G-A Inborn genetic diseases Uncertain significance (Aug 11, 2022)2306662
11-66058971-G-A Inborn genetic diseases Uncertain significance (Dec 12, 2023)3160814

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SF3B2protein_codingprotein_codingENST00000322535 2218580
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00008001257110371257480.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.682915300.5500.00003095831
Missense in Polyphen75179.340.41821931
Synonymous-0.4112031961.040.00001071760
Loss of Function6.00653.20.1130.00000305590

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006850.0000615
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.0001430.000139
European (Non-Finnish)0.0002740.000246
Middle Eastern0.0002180.000217
South Asian0.000.00
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). May also be involved in the assembly of the 'E' complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077). {ECO:0000269|PubMed:10882114, ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:27720643}.;
Pathway
Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.177

Intolerance Scores

loftool
0.0547
rvis_EVS
-1.09
rvis_percentile_EVS
7.11

Haploinsufficiency Scores

pHI
0.144
hipred
Y
hipred_score
0.809
ghis
0.634

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.991

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sf3b2
Phenotype

Gene ontology

Biological process
mRNA splicing, via spliceosome;mRNA processing;RNA splicing;viral process
Cellular component
nucleoplasm;spliceosomal complex;U2 snRNP;U12-type spliceosomal complex;nuclear speck;catalytic step 2 spliceosome
Molecular function
RNA binding;protein binding