SWT1

SWT1 RNA endoribonuclease homolog, the group of Endoribonucleases

Basic information

Region (hg38): 1:185157080-185291781

Previous symbols: [ "C1orf26" ]

Links

ENSG00000116668 ∙ NCBI:54823 ∙ OMIM:619513 ∙ HGNC:16785 ∙ Uniprot:Q5T5J6 ∙ 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 SWT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SWT1 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						0
missense			39	7		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	39	7	0

Variants in SWT1

This is a list of pathogenic ClinVar variants found in the SWT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-185160846-C-A		not specified	Uncertain significance (Aug 08, 2023)
1-185160858-C-G		not specified	Uncertain significance (Oct 16, 2023)
1-185160897-C-A		not specified	Uncertain significance (Feb 16, 2023)
1-185168389-G-A		not specified	Likely benign (Feb 14, 2024)
1-185174401-G-T		not specified	Uncertain significance (Dec 09, 2023)
1-185174418-T-A		not specified	Uncertain significance (Nov 21, 2023)
1-185174494-C-G		not specified	Uncertain significance (Apr 15, 2024)
1-185174527-G-A		not specified	Uncertain significance (Aug 30, 2021)
1-185174653-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-185174688-G-C		not specified	Uncertain significance (Oct 05, 2022)
1-185174757-G-A		not specified	Uncertain significance (May 25, 2022)
1-185174785-A-G		not specified	Uncertain significance (Nov 10, 2022)
1-185174805-A-G		not specified	Uncertain significance (Feb 12, 2024)
1-185174818-C-G		not specified	Uncertain significance (Sep 15, 2021)
1-185174859-A-G		not specified	Likely benign (Oct 25, 2022)
1-185174881-A-G		not specified	Uncertain significance (Jan 09, 2024)
1-185174920-A-G		not specified	Uncertain significance (Oct 12, 2021)
1-185174947-G-A		not specified	Likely benign (Feb 14, 2023)
1-185174985-A-C		not specified	Uncertain significance (Mar 28, 2024)
1-185175004-A-G		not specified	Uncertain significance (Jul 06, 2021)
1-185175031-G-A		not specified	Likely benign (Jun 07, 2024)
1-185175033-A-T		not specified	Uncertain significance (Jun 03, 2022)
1-185175054-A-G		not specified	Uncertain significance (Jun 16, 2024)
1-185175079-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-185180404-C-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SWT1	protein_coding	protein_coding	ENST00000367500	18	134686

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00241	125714	0	12	125726	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	344	431	0.798	0.0000204	5942
Missense in Polyphen		50	116	0.43103		1687
Synonymous	0.505	143	151	0.948	0.00000716	1588
Loss of Function	5.32	6	44.1	0.136	0.00000202	630

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000637	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000630	0.0000615
Middle Eastern	0.000110	0.000109
South Asian	0.0000338	0.0000327
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.53

Haploinsufficiency Scores

• pHI: 0.0522
• hipred: N
• hipred_score: 0.233
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Swt1

Gene ontology

• Biological process: transcription, DNA-templated
• Cellular component: nucleus