INTS4

integrator complex subunit 4, the group of Armadillo like helical domain containing|Integrator complex

Basic information

Region (hg38): 11:77874417-77994715

Links

ENSG00000149262 ∙ NCBI:92105 ∙ OMIM:611348 ∙ HGNC:25048 ∙ Uniprot:Q96HW7 ∙ 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 INTS4 gene.

• Inborn genetic diseases (29 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS4 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				2		2
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	29	3	0

Variants in INTS4

This is a list of pathogenic ClinVar variants found in the INTS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-77878990-G-C		not specified	Uncertain significance (Oct 03, 2022)
11-77879019-C-T		not specified	Uncertain significance (Aug 26, 2022)
11-77879064-C-T		not specified	Uncertain significance (Dec 15, 2023)
11-77879076-C-A		not specified	Uncertain significance (Jun 24, 2022)
11-77879116-C-G		not specified	Uncertain significance (May 31, 2023)
11-77883873-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-77891335-T-A		not specified	Uncertain significance (Feb 23, 2023)
11-77891405-G-A		not specified	Uncertain significance (Feb 27, 2024)
11-77891428-G-A		not specified	Uncertain significance (May 15, 2023)
11-77891459-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-77891462-T-C		not specified	Uncertain significance (Nov 08, 2022)
11-77891739-T-C		not specified	Uncertain significance (Oct 03, 2023)
11-77891764-T-C		not specified	Uncertain significance (Sep 17, 2021)
11-77891772-C-T		not specified	Uncertain significance (Aug 15, 2023)
11-77891775-G-A		not specified	Uncertain significance (May 18, 2023)
11-77891776-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-77891791-G-C		not specified	Uncertain significance (Sep 21, 2021)
11-77891830-C-T		not specified	Uncertain significance (Feb 10, 2022)
11-77894300-A-G		not specified	Uncertain significance (Jul 12, 2023)
11-77900570-G-A			Likely benign (Mar 01, 2023)
11-77901519-C-T		not specified	Uncertain significance (Oct 17, 2023)
11-77903546-C-T			Likely benign (Mar 01, 2023)
11-77907739-C-T		not specified	Uncertain significance (Dec 05, 2022)
11-77918878-T-C		not specified	Uncertain significance (Jun 07, 2023)
11-77921357-G-A		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS4	protein_coding	protein_coding	ENST00000534064	23	115959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-11	1.00	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	433	513	0.844	0.0000267	6281
Missense in Polyphen		92	138.86	0.66252		1735
Synonymous	1.38	162	186	0.871	0.00000930	1884
Loss of Function	3.33	27	53.2	0.507	0.00000304	622

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000479	0.000479
Ashkenazi Jewish	0.00	0.00
East Asian	0.000383	0.000381
Finnish	0.000787	0.000786
European (Non-Finnish)	0.000363	0.000352
Middle Eastern	0.000383	0.000381
South Asian	0.000360	0.000359
Other	0.000327	0.000326

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: 0.153

Intolerance Scores

• loftool: 0.410
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.78

Haploinsufficiency Scores

• pHI: 0.169
• hipred: Y
• hipred_score: 0.575
• ghis: 0.633

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints4

Gene ontology

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