INTS5

integrator complex subunit 5, the group of Integrator complex|Armadillo like helical domain containing

Basic information

Region (hg38): 11:62646848-62653302

Previous symbols: [ "KIAA1698" ]

Links

ENSG00000185085 ∙ NCBI:80789 ∙ OMIM:611349 ∙ HGNC:29352 ∙ Uniprot:Q6P9B9 ∙ 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 INTS5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS5 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				4	2	6
missense			77	1		78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	77	5	2

Variants in INTS5

This is a list of pathogenic ClinVar variants found in the INTS5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62647033-C-T		not specified	Uncertain significance (Aug 05, 2024)
11-62647062-G-C		not specified	Uncertain significance (Feb 07, 2023)
11-62647093-A-G		not specified	Uncertain significance (Dec 20, 2024)
11-62647096-T-C		not specified	Uncertain significance (May 10, 2022)
11-62647107-G-A			Likely benign (Oct 01, 2022)
11-62647124-C-A		not specified	Uncertain significance (Aug 30, 2021)
11-62647150-C-T		not specified	Uncertain significance (Apr 24, 2024)
11-62647198-A-G		not specified	Uncertain significance (Apr 28, 2022)
11-62647229-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-62647238-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-62647250-G-A		not specified	Uncertain significance (Nov 28, 2024)
11-62647256-G-C		not specified	Uncertain significance (Jan 19, 2025)
11-62647339-A-G		not specified	Uncertain significance (Dec 15, 2024)
11-62647361-A-T		not specified	Uncertain significance (Oct 26, 2022)
11-62647364-C-A		not specified	Uncertain significance (Jul 22, 2024)
11-62647370-G-A			Likely benign (Apr 01, 2023)
11-62647385-G-A		not specified	Uncertain significance (May 10, 2024)
11-62647433-C-T		not specified	Uncertain significance (Jan 26, 2023)
11-62647445-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-62647454-C-A		not specified	Uncertain significance (Feb 28, 2023)
11-62647484-C-G		not specified	Uncertain significance (Jan 03, 2024)
11-62647524-G-A			Likely benign (Aug 01, 2022)
11-62647559-C-T		not specified	Uncertain significance (Jan 21, 2025)
11-62647571-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-62647582-G-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS5	protein_coding	protein_coding	ENST00000330574	2	6455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.513	0.486	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	466	584	0.798	0.0000365	6399
Missense in Polyphen		136	216.17	0.62914		2457
Synonymous	-1.42	273	245	1.12	0.0000136	2431
Loss of Function	3.87	6	28.2	0.213	0.00000203	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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: 0.129

Intolerance Scores

• loftool: 0.0476
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.95

Haploinsufficiency Scores

• pHI: 0.316
• hipred: Y
• hipred_score: 0.785
• ghis: 0.560

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints5

Zebrafish Information Network

• Gene name: ints5
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: snRNA processing;snRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytoplasm;membrane;integral component of membrane;nuclear membrane;integrator complex
• Molecular function: protein binding