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GeneBe

SF3B1

splicing factor 3b subunit 1, the group of B-WICH chromatin-remodelling complex subunits|SF3b complex|Armadillo like helical domain containing

Basic information

Region (hg38): 2:197388514-197435079

Links

ENSG00000115524NCBI:23451OMIM:605590HGNC:10768Uniprot:O75533AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SF3B1 gene.

  • not provided (18 variants)
  • Inborn genetic diseases (4 variants)
  • not specified (3 variants)
  • Acute myeloid leukemia (3 variants)
  • Myelodysplastic syndrome (2 variants)
  • SF3B1-related condition (2 variants)
  • Transitional cell carcinoma of the bladder (1 variants)
  • Uveal melanoma (1 variants)
  • B-cell chronic lymphocytic leukemia (1 variants)
  • Chronic myelogenous leukemia, BCR-ABL1 positive (1 variants)
  • Myelodysplastic syndrome progressed to acute myeloid leukemia (1 variants)
  • Adenoid cystic carcinoma (1 variants)
  • Malignant melanoma of skin (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3B1 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
2
clinvar
11
clinvar
14
missense
2
clinvar
8
clinvar
10
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
0
Total 0 2 10 2 11

Variants in SF3B1

This is a list of pathogenic ClinVar variants found in the SF3B1 region.

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

Position Type Phenotype Significance ClinVar
2-197392312-A-G Benign (Jul 27, 2018)788087
2-197392351-G-A Benign (Dec 31, 2019)790342
2-197393071-T-C SF3B1-related condition Benign (Oct 17, 2019)1250652
2-197393196-G-A Benign (Dec 31, 2019)785855
2-197398016-T-C SF3B1-related condition Uncertain significance (Sep 20, 2022)2636431
2-197398035-A-G Benign (Dec 31, 2019)715640
2-197398499-T-C SF3B1-related condition Likely benign (Oct 28, 2019)3035547
2-197400047-T-C SF3B1-related condition Likely benign (Mar 22, 2019)3043892
2-197400137-T-C SF3B1-related condition Likely benign (Apr 25, 2019)3042526
2-197400802-A-G SF3B1-related condition Benign (Nov 01, 2019)1228123
2-197400846-G-A not specified Uncertain significance (Jul 28, 2021)917660
2-197401887-C-T B-cell chronic lymphocytic leukemia • Papillary renal cell carcinoma type 1 Likely pathogenic (May 31, 2016)376530
2-197402097-A-C Uncertain significance (Jul 01, 2017)809134
2-197402104-G-T Benign (Dec 31, 2019)788088
2-197402108-T-A Acute myeloid leukemia Likely pathogenic (Oct 02, 2014)376040
2-197402108-T-G Acute myeloid leukemia Likely pathogenic (Oct 02, 2014)376041
2-197402109-T-A Acute myeloid leukemia Likely pathogenic (Oct 02, 2014)376042
2-197402109-T-C Acute myeloid leukemia Likely pathogenic (Oct 02, 2014)376043
2-197402109-T-G Acute myeloid leukemia Likely pathogenic (Oct 02, 2014)376044
2-197402110-T-A Acute myeloid leukemia Likely pathogenic (Oct 02, 2014)376045
2-197402110-T-C Acute myeloid leukemia • Chronic myelogenous leukemia, BCR-ABL1 positive • SF3B1-related condition Conflicting classifications of pathogenicity (Dec 08, 2022)376004
2-197402110-T-G Acute myeloid leukemia Likely pathogenic (Oct 02, 2014)376046
2-197402138-A-T SF3B1-related condition Likely benign (Apr 25, 2019)3041954
2-197402635-C-A Myelodysplastic syndrome progressed to acute myeloid leukemia • Acute myeloid leukemia • Myelodysplastic syndrome Pathogenic/Likely pathogenic (Oct 10, 2021)219098
2-197402635-C-G Acute myeloid leukemia Pathogenic/Likely pathogenic (Jun 08, 2023)376005

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SF3B1protein_codingprotein_codingENST00000335508 2545308
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.001.79e-11125697021256990.00000796
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense7.701417240.1950.00003798501
Missense in Polyphen22241.670.0910312804
Synonymous0.2802322370.9770.00001212539
Loss of Function7.76172.10.01390.00000424823

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001790.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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;B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.230

Intolerance Scores

loftool
rvis_EVS
-1.13
rvis_percentile_EVS
6.43

Haploinsufficiency Scores

pHI
0.996
hipred
Y
hipred_score
0.859
ghis
0.689

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.963

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sf3b1
Phenotype
homeostasis/metabolism phenotype; skeleton phenotype; hematopoietic 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); immune system phenotype;

Zebrafish Information Network

Gene name
sf3b1
Affected structure
nucleate erythrocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;positive regulation of gene expression, epigenetic
Cellular component
nucleus;nucleoplasm;spliceosomal complex;U2 snRNP;U12-type spliceosomal complex;nuclear speck;U11/U12 snRNP;U2-type prespliceosome;U2-type precatalytic spliceosome;catalytic step 2 spliceosome
Molecular function
RNA binding;mRNA binding;protein binding