ICE1
protein-codinginteractor of little elongation complex ELL subunit 1
Gene summary
Enables protein-macromolecule adaptor activity. Involved in several processes, including positive regulation of intracellular protein transport; positive regulation of transcription by RNA polymerase III; and snRNA transcription. Located in Cajal body; euchromatin; and histone locus body. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Jul 2025]
- KIAA0947
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~69.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0001071
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ICE1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015325.3. 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 | 4 | 6 | 1 | 11 | ||
| missense | 308 | 31 | 4 | 343 | ||
| nonsense | 5 | 5 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 323 | 37 | 5 | 365 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056140.1 | 19 | MANE Select | |
| Ensembl | ENSP00000296564.7 | 19 | MANE Select | |
| Ensembl | ENSP00000485617.1 | 7 | Standard | |
| Ensembl | ENSP00000805137.1 | 19 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ice1 | Danio rerio | Structure: liver Quality: quality abnormal |
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
- positive regulation of protein complex assembly
- snRNA transcription by RNA polymerase II
- snRNA transcription by RNA polymerase III
- positive regulation of transcription by RNA polymerase III
- positive regulation of intracellular protein transport
Molecular Function
- protein binding
- protein homodimerization activity
Cellular Component
- nucleoplasm
- transcription elongation factor complex
- Cajal body
- nuclear body
- transcriptionally active chromatin
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296564
- Coding exons
- 19
- Length
- 69571
- Individuals with no LoFs
- 124614
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 31
- Defined
- 124645
- p
- 0.000124
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.729 | 1069 | 1.14e+3 | 0.939 | 0.0000577 | 14783 |
| Missense (PolyPhen) | 216 | 345.57 | 0.62506 | 4860 | ||
| Synonymous | 0.781 | 410 | 431 | 0.952 | 0.0000239 | 4435 |
| Loss of Function | 7.57 | 7 | 80.2 | 0.0873 | 0.00000406 | 1146 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00023 | 0.00023 | rare |
| Ashkenazi Jewish | 0.00031 | 0.00030 | rare |
| East Asian | 0.00028 | 0.00028 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:22195968, PubMed:23932780). Specifically acts as a scaffold protein that promotes the LEC complex formation and recruitment and RNA polymerase II occupancy at snRNA genes in subnuclear bodies (PubMed:23932780). {ECO:0000269|PubMed:22195968, ECO:0000269|PubMed:23932780}.;
Intolerance Scores
- RVIS EVS
- -0.17
- RVIS percentile EVS
- 40.58
Essentials
- Essential (gene trap)
- E