BYSL

bystin like, the group of SSU processome

Basic information

Region (hg38): 6:41921229-41933050

Links

ENSG00000112578 ∙ NCBI:705 ∙ OMIM:603871 ∙ HGNC:1157 ∙ Uniprot:Q13895 ∙ 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 BYSL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BYSL 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			20	2	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	1

Variants in BYSL

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

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

Position	Type	Phenotype	Significance	ClinVar
6-41921585-G-A		not specified	Uncertain significance (Jun 07, 2024)
6-41921626-C-G		not specified	Uncertain significance (Apr 11, 2023)
6-41921659-G-T		not specified	Uncertain significance (May 13, 2024)
6-41921662-C-T		not specified	Uncertain significance (Apr 01, 2024)
6-41921749-C-T		not specified	Uncertain significance (Mar 29, 2023)
6-41921770-G-C		not specified	Uncertain significance (Apr 23, 2024)
6-41921774-C-G		not specified	Uncertain significance (May 02, 2024)
6-41921822-C-T		not specified	Uncertain significance (Dec 28, 2023)
6-41927379-A-G		not specified	Likely benign (Feb 17, 2024)
6-41927455-C-T			Benign (May 02, 2018)
6-41930134-G-A		not specified	Uncertain significance (Jun 07, 2023)
6-41930184-G-A		not specified	Uncertain significance (Dec 01, 2022)
6-41930189-G-C		not specified	Uncertain significance (Mar 24, 2023)
6-41930220-A-G		not specified	Uncertain significance (Apr 26, 2024)
6-41930266-G-A		not specified	Uncertain significance (Nov 01, 2022)
6-41930641-T-C		not specified	Uncertain significance (Dec 19, 2023)
6-41930650-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-41930651-G-T		not specified	Uncertain significance (Aug 28, 2023)
6-41930692-C-T		not specified	Uncertain significance (Nov 12, 2021)
6-41930699-A-G		not specified	Uncertain significance (Jun 29, 2023)
6-41930703-G-C		not specified	Uncertain significance (Mar 25, 2024)
6-41931475-G-A		not specified	Likely benign (Nov 10, 2022)
6-41931491-G-A		not specified	Uncertain significance (May 18, 2022)
6-41931781-A-G		not specified	Uncertain significance (Mar 21, 2022)
6-41932404-A-T		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BYSL	protein_coding	protein_coding	ENST00000230340	7	11859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000996	0.988	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.488	243	265	0.916	0.0000155	2797
Missense in Polyphen		87	102.13	0.85188		1132
Synonymous	0.786	99	109	0.904	0.00000617	921
Loss of Function	2.23	10	21.0	0.475	0.00000126	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.000165	0.000163
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for processing of 20S pre-rRNA precursor and biogenesis of 40S ribosomal subunits. May be required for trophinin-dependent regulation of cell adhesion during implantation of human embryos. {ECO:0000269|PubMed:17360433, ECO:0000269|PubMed:17381424}.

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.646
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.85

Haploinsufficiency Scores

• pHI: 0.603
• hipred: Y
• hipred_score: 0.694
• ghis: 0.539

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bysl
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: bysl
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);trophectodermal cell differentiation;rRNA processing;cell adhesion;female pregnancy;cell population proliferation
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;membrane;preribosome, small subunit precursor;intracellular membrane-bounded organelle;apical part of cell
• Molecular function: RNA binding;protein binding;snoRNA binding