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): 2:197388515-197435079
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (23 variants)
- not_provided (16 variants)
- SF3B1-related_disorder (10 variants)
- Myelodysplastic_syndrome (6 variants)
- Neurodevelopmental_disorder (1 variants)
- Chronic_myelogenous_leukemia,_BCR-ABL1_positive (1 variants)
- Myelodysplastic_syndrome_progressed_to_acute_myeloid_leukemia (1 variants)
- Acute_myeloid_leukemia (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 SF3B1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012433.4. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 13 | |||||
| missense | 28 | 33 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 5 | 30 | 6 | 7 |
Highest pathogenic variant AF is 0.000044885262
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SF3B1 | protein_coding | protein_coding | ENST00000335508 | 25 | 45308 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 1.79e-11 | 125697 | 0 | 2 | 125699 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 7.70 | 141 | 724 | 0.195 | 0.0000379 | 8501 |
| Missense in Polyphen | 22 | 241.67 | 0.091031 | 2804 | ||
| Synonymous | 0.280 | 232 | 237 | 0.977 | 0.0000121 | 2539 |
| Loss of Function | 7.76 | 1 | 72.1 | 0.0139 | 0.00000424 | 823 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000179 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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