INTS2

integrator complex subunit 2, the group of Integrator complex

Basic information

Region (hg38): 17:61865367-61928016

Previous symbols: [ "KIAA1287" ]

Links

ENSG00000108506NCBI:57508OMIM:611346HGNC:29241Uniprot:Q9H0H0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INTS2 gene.

  • not_specified (106 variants)
  • not_provided (2 variants)
  • INTS2-related_disorder (2 variants)
  • Exstrophy-epispadias_complex (1 variants)

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. These statistics are base on transcript: NM_001351695.2. 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
1
clinvar
1
missense
103
clinvar
3
clinvar
1
clinvar
107
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 103 4 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
INTS2protein_codingprotein_codingENST00000444766 2562647
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9970.003021246280311246590.000124
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.264596170.7440.00003187836
Missense in Polyphen134232.640.575992973
Synonymous1.551852140.8650.00001082315
Loss of Function6.061061.10.1640.00000331741

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001280.000127
Ashkenazi Jewish0.00009940.0000994
East Asian0.0001130.000111
Finnish0.0001860.000186
European (Non-Finnish)0.0001550.000150
Middle Eastern0.0001130.000111
South Asian0.00007830.0000654
Other0.0003400.000330

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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