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.

• not_specified (101 variants)

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. These statistics are base on transcript: NM_000017673.7. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			87	13		100
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	87	14	0

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