GeneBe

INTS3

integrator complex subunit 3, the group of Integrator complex

Basic information

Region (hg38): 1:153728050-153774808

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.

  • not_specified (44 variants)
  • Prostate_cancer (1 variants)
  • Myoepithelial_tumor (1 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. These statistics are base on transcript: NM_000023015.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
46
clinvar
 46
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 46 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
INTS3protein_codingprotein_codingENST00000318967 3046013
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.000.0002831257260221257480.0000875
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense4.412935960.4910.00003406860
Missense in Polyphen67210.540.318242389
Synonymous1.072132340.9110.00001342000
Loss of Function6.481067.50.1480.00000379713

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008680.0000868
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.0001230.000123
Middle Eastern0.00005440.0000544
South Asian0.00006530.0000653
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ints3
Phenotype

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