SART1

spliceosome associated factor 1, recruiter of U4/U6.U5 tri-snRNP, the group of tri-snRP complex

Basic information

Region (hg38): 11:65961728-65980137

Links

ENSG00000175467NCBI:9092OMIM:605941HGNC:10538Uniprot:O43290AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SART1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SART1 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
missense
52
clinvar
52
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 52 1 0

Variants in SART1

This is a list of pathogenic ClinVar variants found in the SART1 region.

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

Position Type Phenotype Significance ClinVar
11-65961838-G-T not specified Uncertain significance (Feb 28, 2024)3157868
11-65961839-C-T not specified Uncertain significance (Dec 27, 2023)3157869
11-65961856-A-G not specified Uncertain significance (Dec 01, 2022)2330556
11-65961920-G-A not specified Uncertain significance (Feb 07, 2023)3157857
11-65961949-C-T not specified Uncertain significance (Aug 11, 2022)2359134
11-65961961-G-A not specified Uncertain significance (Apr 12, 2024)3316169
11-65961977-G-A not specified Uncertain significance (Nov 21, 2022)2329170
11-65962001-C-T not specified Uncertain significance (Jul 26, 2022)2210136
11-65962034-A-C not specified Uncertain significance (Dec 13, 2022)2401623
11-65962035-G-C not specified Uncertain significance (Dec 13, 2022)2401625
11-65962051-C-T not specified Uncertain significance (Aug 04, 2021)2402389
11-65964120-C-G not specified Uncertain significance (Jun 11, 2021)2315851
11-65965095-C-T not specified Uncertain significance (Jun 06, 2023)2535408
11-65965140-T-C not specified Uncertain significance (Oct 04, 2022)2316879
11-65965155-G-C not specified Uncertain significance (Jun 02, 2023)2555544
11-65965356-T-G not specified Uncertain significance (Dec 21, 2023)3157867
11-65965382-G-A not specified Uncertain significance (Mar 27, 2023)2569826
11-65965745-C-T not specified Uncertain significance (Aug 09, 2021)2218270
11-65965759-G-A not specified Uncertain significance (Jun 30, 2023)2592789
11-65965763-T-C not specified Uncertain significance (May 08, 2024)3316171
11-65965775-G-A not specified Uncertain significance (Nov 30, 2022)2411192
11-65965917-C-T not specified Uncertain significance (Jan 04, 2022)3157870
11-65966078-G-A not specified Uncertain significance (Dec 15, 2023)3157871
11-65966111-G-A not specified Uncertain significance (Mar 23, 2022)2409918
11-65966417-G-A not specified Uncertain significance (Mar 07, 2023)2495119

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SART1protein_codingprotein_codingENST00000312397 2018140
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8820.1181257070121257190.0000477
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.303494930.7080.00003265119
Missense in Polyphen120213.840.561162152
Synonymous-0.5322242141.050.00001451586
Loss of Function5.10946.60.1930.00000267517

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002230.000214
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005330.0000528
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.0001670.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in mRNA splicing as a component of the U4/U6-U5 tri-snRNP, one of the building blocks of the spliceosome. May also bind to DNA. {ECO:0000269|PubMed:11350945}.;
Pathway
Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.104

Intolerance Scores

loftool
0.336
rvis_EVS
-0.95
rvis_percentile_EVS
9.32

Haploinsufficiency Scores

pHI
0.817
hipred
Y
hipred_score
0.747
ghis
0.536

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.850

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sart1
Phenotype

Gene ontology

Biological process
spliceosomal snRNP assembly;mRNA splicing, via spliceosome;maturation of 5S rRNA;mRNA cis splicing, via spliceosome;positive regulation of cytotoxic T cell differentiation
Cellular component
nucleus;nucleoplasm;cytoplasm;Golgi apparatus;cytosol;Cajal body;nuclear speck;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome;catalytic step 2 spliceosome
Molecular function
RNA binding;protein binding