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

ENSG00000175467 ∙ NCBI:9092 ∙ OMIM:605941 ∙ HGNC:10538 ∙ Uniprot:O43290 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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		1
missense			38			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
11-65961838-G-T		not specified	Uncertain significance (Feb 28, 2024)
11-65961839-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-65961856-A-G		not specified	Uncertain significance (Dec 01, 2022)
11-65961920-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-65961949-C-T		not specified	Uncertain significance (Aug 11, 2022)
11-65961977-G-A		not specified	Uncertain significance (Nov 21, 2022)
11-65962001-C-T		not specified	Uncertain significance (Jul 26, 2022)
11-65962034-A-C		not specified	Uncertain significance (Dec 13, 2022)
11-65962035-G-C		not specified	Uncertain significance (Dec 13, 2022)
11-65962051-C-T		not specified	Uncertain significance (Aug 04, 2021)
11-65964120-C-G		not specified	Uncertain significance (Jun 11, 2021)
11-65965095-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-65965140-T-C		not specified	Uncertain significance (Oct 04, 2022)
11-65965155-G-C		not specified	Uncertain significance (Jun 02, 2023)
11-65965356-T-G		not specified	Uncertain significance (Dec 21, 2023)
11-65965382-G-A		not specified	Uncertain significance (Mar 27, 2023)
11-65965745-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-65965759-G-A		not specified	Uncertain significance (Jun 30, 2023)
11-65965775-G-A		not specified	Uncertain significance (Nov 30, 2022)
11-65965917-C-T		not specified	Uncertain significance (Jan 04, 2022)
11-65966078-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-65966111-G-A		not specified	Uncertain significance (Mar 23, 2022)
11-65966417-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-65966421-G-C		not specified	Uncertain significance (Dec 02, 2022)
11-65966456-G-A		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sart1

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