SART1
Basic information
Region (hg38): 11:65961728-65980137
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 108 | 110 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 108 | 4 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SART1 | protein_coding | protein_coding | ENST00000312397 | 20 | 18140 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.882 | 0.118 | 125707 | 0 | 12 | 125719 | 0.0000477 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.30 | 349 | 493 | 0.708 | 0.0000326 | 5119 |
Missense in Polyphen | 120 | 213.84 | 0.56116 | 2152 | ||
Synonymous | -0.532 | 224 | 214 | 1.05 | 0.0000145 | 1586 |
Loss of Function | 5.10 | 9 | 46.6 | 0.193 | 0.00000267 | 517 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000223 | 0.000214 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000533 | 0.0000528 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.000167 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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