SF3B1
Basic information
Region (hg38): 2:197388515-197435079
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 10 | 17 | ||||
missense | 11 | |||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 2 | 2 | 4 | |||
non coding | 0 | |||||
Total | 0 | 2 | 11 | 6 | 10 |
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) | |||
2-197392351-G-A | Benign (Dec 31, 2019) | |||
2-197393071-T-C | SF3B1-related disorder | Benign (Oct 17, 2019) | ||
2-197393196-G-A | Benign (Dec 31, 2019) | |||
2-197398016-T-C | SF3B1-related disorder | Uncertain significance (Sep 20, 2022) | ||
2-197398035-A-G | Benign (Dec 31, 2019) | |||
2-197398499-T-C | SF3B1-related disorder | Likely benign (Oct 28, 2019) | ||
2-197400047-T-C | SF3B1-related disorder | Likely benign (Mar 22, 2019) | ||
2-197400137-T-C | SF3B1-related disorder | Likely benign (Apr 25, 2019) | ||
2-197400802-A-G | SF3B1-related disorder | Benign (Nov 01, 2019) | ||
2-197400846-G-A | not specified | Uncertain significance (Jul 28, 2021) | ||
2-197401887-C-T | B-cell chronic lymphocytic leukemia • Papillary renal cell carcinoma type 1 | Likely pathogenic (May 31, 2016) | ||
2-197402097-A-C | Uncertain significance (Jul 01, 2017) | |||
2-197402101-T-G | Neurodevelopmental disorder | Uncertain significance (Jun 19, 2024) | ||
2-197402104-G-T | Benign (Dec 31, 2019) | |||
2-197402108-T-A | Acute myeloid leukemia | Likely pathogenic (Oct 02, 2014) | ||
2-197402108-T-G | Acute myeloid leukemia | Likely pathogenic (Oct 02, 2014) | ||
2-197402109-T-A | Acute myeloid leukemia | Likely pathogenic (Oct 02, 2014) | ||
2-197402109-T-C | Acute myeloid leukemia | Likely pathogenic (Oct 02, 2014) | ||
2-197402109-T-G | Acute myeloid leukemia | Likely pathogenic (Oct 02, 2014) | ||
2-197402110-T-A | Acute myeloid leukemia | Likely pathogenic (Oct 02, 2014) | ||
2-197402110-T-C | Acute myeloid leukemia • Chronic myelogenous leukemia, BCR-ABL1 positive • SF3B1-related disorder | Conflicting classifications of pathogenicity (Dec 08, 2022) | ||
2-197402110-T-G | Acute myeloid leukemia | Likely pathogenic (Oct 02, 2014) | ||
2-197402138-A-T | SF3B1-related disorder | Likely benign (Apr 25, 2019) | ||
2-197402635-C-A | Myelodysplastic syndrome progressed to acute myeloid leukemia • Acute myeloid leukemia • Myelodysplastic syndrome | Pathogenic/Likely pathogenic (Oct 10, 2021) |
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