INTS11

integrator complex subunit 11, the group of MBL fold containing DNA/RNA interacting subfamily|MicroRNA protein coding host genes|Integrator complex

Basic information

Region (hg38): 1:1311584-1324687

Previous symbols: [ "CPSF3L" ]

Links

ENSG00000127054 ∙ NCBI:54973 ∙ OMIM:611354 ∙ HGNC:26052 ∙ Uniprot:Q5TA45 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	37054711

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INTS11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS11 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	2	3
missense			49			49
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	0	1	49	2	3

Variants in INTS11

This is a list of pathogenic ClinVar variants found in the INTS11 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1311873-G-C		not specified	Uncertain significance (May 27, 2022)
1-1311922-G-A			Benign (Jun 26, 2018)
1-1312109-C-T		not specified	Uncertain significance (Dec 11, 2023)
1-1312115-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-1312134-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-1312139-T-C		not specified	Uncertain significance (Sep 14, 2022)
1-1312208-G-T			Benign (Jul 03, 2018)
1-1312238-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-1312247-C-T		not specified	Uncertain significance (May 24, 2023)
1-1312250-A-G		not specified	Uncertain significance (Jan 08, 2024)
1-1312260-C-G		not specified	Uncertain significance (Aug 24, 2023)
1-1312287-G-A		not specified	Uncertain significance (Nov 18, 2023)
1-1312290-C-T		Neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities • not specified	Uncertain significance (Nov 19, 2022)
1-1312293-G-A		not specified	Uncertain significance (May 23, 2023)
1-1312308-G-C		not specified	Uncertain significance (Apr 06, 2024)
1-1312441-C-T		not specified	Uncertain significance (May 13, 2024)
1-1312451-T-C		not specified	Uncertain significance (Sep 17, 2021)
1-1312475-G-A		not specified	Uncertain significance (Dec 21, 2022)
1-1312486-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-1312487-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-1312501-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-1312594-C-G		not specified	Uncertain significance (Sep 14, 2022)
1-1312608-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-1312648-G-C		not specified	Uncertain significance (Oct 17, 2023)
1-1312667-G-A		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS11	protein_coding	protein_coding	ENST00000540437	17	13107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.99e-14	0.571	125531	0	144	125675	0.000573

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.544	357	387	0.922	0.0000251	3945
Missense in Polyphen		127	160.49	0.79132		1522
Synonymous	-4.01	228	163	1.40	0.0000119	1150
Loss of Function	1.58	26	36.3	0.717	0.00000218	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000729	0.000695
Ashkenazi Jewish	0.0000997	0.0000993
East Asian	0.000606	0.000598
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000737	0.000722
Middle Eastern	0.000606	0.000598
South Asian	0.000623	0.000621
Other	0.00134	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic 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. Mediates the snRNAs 3' cleavage. Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:16239144, ECO:0000269|PubMed:23904267}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -1.82
• rvis_percentile_EVS: 2.16

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.533
• ghis: 0.630

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Ints11

Zebrafish Information Network

• Gene name: ints11
• 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;cytoplasm;cytosol;integrator complex;blood microparticle
• Molecular function: protein binding;hydrolase activity