INTS2

integrator complex subunit 2, the group of Integrator complex

Basic information

Region (hg38): 17:61865367-61928016

Previous symbols: [ "KIAA1287" ]

Links

ENSG00000108506 ∙ NCBI:57508 ∙ OMIM:611346 ∙ HGNC:29241 ∙ Uniprot:Q9H0H0 ∙ 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 INTS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS2 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	2
missense			43	2	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding						0
Total	0	0	43	3	2

Variants in INTS2

This is a list of pathogenic ClinVar variants found in the INTS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-61867702-G-C		not specified	Uncertain significance (Sep 27, 2022)
17-61867863-G-T		not specified	Uncertain significance (Jun 11, 2024)
17-61867898-T-C		not specified	Uncertain significance (Nov 09, 2021)
17-61867934-G-A		not specified	Uncertain significance (May 24, 2023)
17-61867989-A-G		not specified	Uncertain significance (Oct 06, 2021)
17-61868006-A-G		not specified	Uncertain significance (Dec 08, 2023)
17-61869057-T-C		not specified	Uncertain significance (Aug 28, 2024)
17-61869099-T-C		not specified	Uncertain significance (May 21, 2024)
17-61869117-G-C		not specified	Uncertain significance (Feb 13, 2024)
17-61869135-A-T		not specified	Uncertain significance (Mar 04, 2024)
17-61869139-T-G		not specified	Uncertain significance (Feb 15, 2023)
17-61869782-T-G		not specified	Uncertain significance (Jun 10, 2024)
17-61869798-C-T		not specified	Uncertain significance (May 23, 2023)
17-61869827-A-C		not specified	Uncertain significance (Apr 05, 2023)
17-61869834-A-C		not specified	Uncertain significance (May 30, 2024)
17-61869952-G-C		not specified	Uncertain significance (Sep 10, 2024)
17-61872290-A-G		not specified	Uncertain significance (Jun 05, 2023)
17-61872335-C-A		not specified	Uncertain significance (Jun 12, 2023)
17-61872344-T-A		not specified	Uncertain significance (Nov 26, 2024)
17-61872347-T-C		not specified	Uncertain significance (Mar 29, 2022)
17-61872381-G-T		not specified	Uncertain significance (Jan 09, 2024)
17-61874956-T-A			Benign (Aug 16, 2018)
17-61877912-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-61877948-G-A		not specified	Uncertain significance (Oct 20, 2021)
17-61877948-G-C		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS2	protein_coding	protein_coding	ENST00000444766	25	62647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00302	124628	0	31	124659	0.000124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	459	617	0.744	0.0000318	7836
Missense in Polyphen		134	232.64	0.57599		2973
Synonymous	1.55	185	214	0.865	0.0000108	2315
Loss of Function	6.06	10	61.1	0.164	0.00000331	741

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000127
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.000113	0.000111
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000155	0.000150
Middle Eastern	0.000113	0.000111
South Asian	0.0000783	0.0000654
Other	0.000340	0.000330

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: 0.130

Intolerance Scores

• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.36

Haploinsufficiency Scores

• pHI: 0.773
• hipred: Y
• hipred_score: 0.736
• ghis: 0.661

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: snRNA processing;snRNA 3'-end 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