SF3B5

splicing factor 3b subunit 5, the group of SF3b complex

Basic information

Region (hg38): 6:144094884-144095573

Links

ENSG00000169976NCBI:83443OMIM:617847HGNC:21083Uniprot:Q9BWJ5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SF3B5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3B5 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
0
missense
4
clinvar
4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 4 0 0

Variants in SF3B5

This is a list of pathogenic ClinVar variants found in the SF3B5 region.

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

Position Type Phenotype Significance ClinVar
6-144095346-T-C not specified Uncertain significance (Nov 07, 2024)3440394
6-144095373-G-A not specified Uncertain significance (Dec 04, 2023)3160837
6-144095374-A-T not specified Uncertain significance (Aug 14, 2024)3440393
6-144095379-T-A not specified Uncertain significance (Mar 12, 2024)3160836

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SF3B5protein_codingprotein_codingENST00000367569 1737
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5840.37800000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.192548.10.5190.00000224574
Missense in Polyphen718.7950.37244213
Synonymous-0.7202319.01.219.84e-7154
Loss of Function1.5302.710.001.17e-730

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)0.000.00
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, a constituent of the spliceosome (PubMed:27720643, PubMed:28781166). 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). {ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:27720643, ECO:0000269|PubMed:28781166}.;
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
0.113

Intolerance Scores

loftool
rvis_EVS
0.1
rvis_percentile_EVS
60.96

Haploinsufficiency Scores

pHI
0.168
hipred
Y
hipred_score
0.788
ghis
0.643

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.977

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Sf3b5
Phenotype

Zebrafish Information Network

Gene name
sf3b5
Affected structure
trunk
Phenotype tag
abnormal
Phenotype quality
atrophied

Gene ontology

Biological process
mRNA splicing, via spliceosome
Cellular component
nucleus;nucleoplasm;U2 snRNP;U12-type spliceosomal complex;U2-type precatalytic spliceosome
Molecular function
RNA binding