INTS3

integrator complex subunit 3, the group of Integrator complex

Basic information

Region (hg38): 1:153728049-153774808

Previous symbols: [ "C1orf60" ]

Links

ENSG00000143624 ∙ NCBI:65123 ∙ OMIM:611347 ∙ HGNC:26153 ∙ Uniprot:Q68E01 ∙ 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 INTS3 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS3 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in INTS3

This is a list of pathogenic ClinVar variants found in the INTS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153728654-A-G		not specified	Uncertain significance (Oct 05, 2021)
1-153728678-C-T		not specified	Uncertain significance (Feb 02, 2022)
1-153728690-C-T		not specified	Uncertain significance (Aug 02, 2023)
1-153728773-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-153741336-C-G		not specified	Uncertain significance (Oct 05, 2021)
1-153746985-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-153751198-C-A		not specified	Uncertain significance (Jan 29, 2024)
1-153757762-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-153760389-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-153760837-A-G		not specified	Uncertain significance (May 11, 2022)
1-153760867-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-153762839-A-G		not specified	Uncertain significance (Dec 14, 2021)
1-153763296-T-C		Malignant tumor of prostate	Uncertain significance (-)
1-153763837-C-T		not specified	Uncertain significance (Oct 20, 2023)
1-153768899-G-A		not specified	Uncertain significance (May 26, 2022)
1-153770211-C-G		not specified	Uncertain significance (Mar 04, 2024)
1-153772398-T-G		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
1-153773204-C-G		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS3	protein_coding	protein_coding	ENST00000318967	30	46013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000283	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.41	293	596	0.491	0.0000340	6860
Missense in Polyphen		67	210.54	0.31824		2389
Synonymous	1.07	213	234	0.911	0.0000134	2000
Loss of Function	6.48	10	67.5	0.148	0.00000379	713

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the Integrator (INT) complex. The Integrator complex is 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: 0.136

Intolerance Scores

• loftool: 0.175
• rvis_EVS: -1.29
• rvis_percentile_EVS: 5.03

Haploinsufficiency Scores

• pHI: 0.517
• hipred: Y
• hipred_score: 0.736
• ghis: 0.555

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints3

Gene ontology

• Biological process: DNA repair;cellular response to DNA damage stimulus;mitotic cell cycle checkpoint;response to ionizing radiation;snRNA processing;snRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;integrator complex;SOSS complex
• Molecular function: protein binding