INTS13

integrator complex subunit 13, the group of Integrator complex

Basic information

Region (hg38): 12:26905181-26938326

Previous symbols: [ "C12orf11", "ASUN" ]

Links

ENSG00000064102NCBI:55726OMIM:615079HGNC:20174Uniprot:Q9NVM9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INTS13 gene.

  • not_specified (47 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018164.3. 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
45
clinvar
1
clinvar
46
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 45 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
INTS13protein_codingprotein_codingENST00000261191 1633146
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8620.1381257310171257480.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.762323840.6040.00002024649
Missense in Polyphen57124.470.457941537
Synonymous-0.2071291261.020.000006341290
Loss of Function4.84841.70.1920.00000249498

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009080.0000908
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0001060.000105
Middle Eastern0.00005440.0000544
South Asian0.00006570.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Crucial regulator of the mitotic cell cycle and development. At prophase, required for dynein anchoring to the nuclear envelope important for proper centrosome-nucleus coupling. At G2/M phase, may be required for proper spindle formation and execution of cytokinesis. Probable 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 (PubMed:23904267). {ECO:0000269|PubMed:15737938, ECO:0000269|PubMed:23097494, ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:23097494, ECO:0000305|PubMed:23904267}.;
Pathway
Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

pRec
0.0908

Intolerance Scores

loftool
rvis_EVS
-0.2
rvis_percentile_EVS
38.82

Haploinsufficiency Scores

pHI
0.642
hipred
Y
hipred_score
0.728
ghis
0.625

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Ints13
Phenotype

Gene ontology

Biological process
mitotic spindle organization;regulation of mitotic cell cycle;flagellated sperm motility;snRNA transcription by RNA polymerase II;cell division;centrosome localization;regulation of fertilization;protein localization to nuclear envelope
Cellular component
nucleus;nucleoplasm;cytoplasm
Molecular function
protein binding