ISY1

ISY1 splicing factor homolog, the group of Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex|Spliceosomal C complex

Basic information

Region (hg38): 3:129127415-129161063

Links

ENSG00000240682 ∙ NCBI:57461 ∙ OMIM:612764 ∙ HGNC:29201 ∙ Uniprot:Q9ULR0 ∙ 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 ISY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISY1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in ISY1

This is a list of pathogenic ClinVar variants found in the ISY1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129134150-C-G		not specified	Uncertain significance (Mar 20, 2024)
3-129137140-C-T		not specified	Uncertain significance (May 18, 2023)
3-129137145-G-A		not specified	Uncertain significance (Apr 08, 2024)
3-129137150-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
3-129137164-C-T		not specified	Uncertain significance (Mar 14, 2024)
3-129137192-C-G		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISY1	protein_coding	protein_coding	ENST00000273541	12	33879

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000102	123526	0	2	123528	0.00000810

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	114	158	0.721	0.00000869	1971
Missense in Polyphen		24	47.623	0.50396		573
Synonymous	1.78	39	55.9	0.698	0.00000322	558
Loss of Function	4.74	0	26.1	0.00	0.00000182	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in pre-mRNA splicing as component of the spliceosome. {ECO:0000305|PubMed:11991638, ECO:0000305|PubMed:25599396}.
• Pathway: Spliceosome - Homo sapiens (human);DNA Repair;Metabolism of RNA;mRNA Splicing - Major Pathway;Formation of TC-NER Pre-Incision Complex;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair (Consensus)

Intolerance Scores

• loftool: 0.397
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.598
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.707

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Isy1

Gene ontology

• Biological process: generation of catalytic spliceosome for second transesterification step;mRNA 3'-splice site recognition;mRNA splicing, via spliceosome;transcription-coupled nucleotide-excision repair
• Cellular component: Prp19 complex;nucleoplasm;catalytic step 2 spliceosome;post-mRNA release spliceosomal complex;post-spliceosomal complex
• Molecular function: first spliceosomal transesterification activity;RNA binding;protein binding