INTS9

integrator complex subunit 9, the group of Integrator complex|MBL fold containing DNA/RNA interacting subfamily

Basic information

Region (hg38): 8:28767661-28890242

Links

ENSG00000104299 ∙ NCBI:55756 ∙ OMIM:611352 ∙ HGNC:25592 ∙ Uniprot:Q9NV88 ∙ 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 INTS9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS9 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			49	2		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	3	0

Variants in INTS9

This is a list of pathogenic ClinVar variants found in the INTS9 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-28768172-C-A		not specified	Uncertain significance (Mar 04, 2025)
8-28768180-C-T		not specified	Uncertain significance (Oct 27, 2022)
8-28768198-A-G		not specified	Uncertain significance (Dec 01, 2022)
8-28768202-C-T		not specified	Uncertain significance (Dec 24, 2024)
8-28768240-A-G		not specified	Uncertain significance (Mar 28, 2024)
8-28768274-C-T		not specified	Uncertain significance (Jan 10, 2023)
8-28768283-C-T		not specified	Uncertain significance (Dec 10, 2024)
8-28768297-T-A		not specified	Uncertain significance (Oct 18, 2021)
8-28769918-C-T		not specified	Uncertain significance (Apr 04, 2023)
8-28769921-G-A		not specified	Uncertain significance (Mar 14, 2023)
8-28769924-T-G		not specified	Uncertain significance (Jul 20, 2022)
8-28769966-C-T		not specified	Likely benign (Jan 08, 2024)
8-28769968-T-C		not specified	Uncertain significance (Nov 08, 2024)
8-28769981-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-28770016-C-T		not specified	Uncertain significance (Aug 01, 2024)
8-28770023-G-T		not specified	Uncertain significance (Dec 16, 2024)
8-28771013-A-C		not specified	Uncertain significance (Jan 08, 2025)
8-28771059-T-A		not specified	Uncertain significance (Sep 10, 2024)
8-28775787-C-T		not specified	Uncertain significance (Mar 08, 2024)
8-28775788-G-A		not specified	Uncertain significance (Jan 10, 2025)
8-28775806-C-T		not specified	Uncertain significance (Dec 16, 2023)
8-28775824-G-A		not specified	Uncertain significance (Apr 08, 2024)
8-28775839-G-C		not specified	Uncertain significance (Dec 17, 2023)
8-28775851-C-T		not specified	Uncertain significance (Nov 29, 2024)
8-28775893-G-T		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS9	protein_coding	protein_coding	ENST00000521022	17	122582

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.32e-7	0.998	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	327	385	0.849	0.0000222	4297
Missense in Polyphen		86	122.26	0.70341		1346
Synonymous	-0.342	166	160	1.03	0.0000104	1298
Loss of Function	2.73	16	32.9	0.486	0.00000140	409

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000430	0.000428
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000327	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000327	0.000217
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.878
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.88

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.700
• ghis: 0.628

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints9

Zebrafish Information Network

• Gene name: ints9
• Affected structure: hemopoiesis
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: snRNA processing;snRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytosol;integrator complex
• Molecular function: protein binding