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.

  • not_specified (111 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. These statistics are base on transcript: NM_000005146.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
108
clinvar
2
clinvar
110
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 108 4 0
Loading clinvar variants...

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