INTS13
protein-codingintegrator complex subunit 13, the group of Integrator complex
Gene summary
Enables DNA-binding transcription factor binding activity. Involved in RNA metabolic process; regulation of mitotic cell cycle; and regulation of transcription elongation by RNA polymerase II. Acts upstream of or within centrosome localization; mitotic spindle organization; and protein localization to nuclear envelope. Located in cytoplasm and nuclear body. Part of INTAC complex and integrator complex. Is active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]
- C12orf11
- ASUN
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0015375
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to INTS13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018164.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 4 | |||
| missense | 58 | 1 | 59 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 64 | 2 | 0 | 66 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060634.2 | 16 | MANE Select | |
| Ensembl | ENSP00000261191.7 | 16 | MANE Select | |
| Ensembl | ENSP00000448985.1 | 5 | Standard | |
| Ensembl | ENSP00000443066.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gene expression (Transcription)
- RNA polymerase II transcribes snRNA genes
- RNA Polymerase II Transcription
Biological Process
- mitotic spindle organization
- regulation of mitotic cell cycle
- flagellated sperm motility
- snRNA transcription by RNA polymerase II
- cell division
Molecular Function
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000261191
- Coding exons
- 16
- Length
- 33146
- Individuals with no LoFs
- 125731
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 17
- Defined
- 125748
- p
- 0.0000676
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.76 | 232 | 384 | 0.604 | 0.0000202 | 4649 |
| Missense (PolyPhen) | 57 | 124.47 | 0.45794 | 1537 | ||
| Synonymous | -0.207 | 129 | 126 | 1.02 | 0.00000634 | 1290 |
| Loss of Function | 4.84 | 8 | 41.7 | 0.192 | 0.00000249 | 498 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.0908
Intolerance Scores
- RVIS EVS
- -0.2
- RVIS percentile EVS
- 38.82
Essentials
- Essential (gene trap)
- E