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GeneBe

SART1

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

Basic information

Region (hg38): 11:65961727-65980137

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.

  • Inborn genetic diseases (38 variants)
  • not provided (1 variants)

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
38
clinvar
38
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 38 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
11-65961856-A-G Inborn genetic diseases Uncertain significance (Dec 01, 2022)2330556
11-65961949-C-T Inborn genetic diseases Uncertain significance (Aug 11, 2022)2359134
11-65961977-G-A Inborn genetic diseases Uncertain significance (Nov 21, 2022)2329170
11-65962001-C-T Inborn genetic diseases Uncertain significance (Jul 26, 2022)2210136
11-65962034-A-C Inborn genetic diseases Uncertain significance (Dec 13, 2022)2401623
11-65962035-G-C Inborn genetic diseases Uncertain significance (Dec 13, 2022)2401625
11-65962051-C-T Inborn genetic diseases Uncertain significance (Aug 04, 2021)2402389
11-65964120-C-G Inborn genetic diseases Uncertain significance (Jun 11, 2021)2315851
11-65965095-C-T Inborn genetic diseases Uncertain significance (Jun 06, 2023)2535408
11-65965140-T-C Inborn genetic diseases Uncertain significance (Oct 04, 2022)2316879
11-65965155-G-C Inborn genetic diseases Uncertain significance (Jun 02, 2023)2555544
11-65965382-G-A Inborn genetic diseases Uncertain significance (Mar 27, 2023)2569826
11-65965745-C-T Inborn genetic diseases Uncertain significance (Aug 09, 2021)2218270
11-65965759-G-A Inborn genetic diseases Uncertain significance (Jun 30, 2023)2592789
11-65965775-G-A Inborn genetic diseases Uncertain significance (Nov 30, 2022)2411192
11-65966111-G-A Inborn genetic diseases Uncertain significance (Mar 23, 2022)2409918
11-65966417-G-A Inborn genetic diseases Uncertain significance (Mar 07, 2023)2495119
11-65966421-G-C Inborn genetic diseases Uncertain significance (Dec 02, 2022)2331676
11-65966456-G-A Inborn genetic diseases Uncertain significance (May 18, 2023)2549005
11-65966512-G-C Inborn genetic diseases Uncertain significance (Oct 27, 2021)2371163
11-65966533-G-A Inborn genetic diseases Uncertain significance (Jun 22, 2023)2605762
11-65967298-C-G Inborn genetic diseases Uncertain significance (Jan 26, 2022)2343245
11-65967299-G-T Inborn genetic diseases Uncertain significance (Feb 07, 2023)2482121
11-65967301-A-G Inborn genetic diseases Uncertain significance (Sep 16, 2021)2250643
11-65967375-T-G Inborn genetic diseases Uncertain significance (Nov 17, 2022)2327183

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