ICE1

Chr 5

interactor of little elongation complex ELL subunit 1

Also known as: KIAA0947

NCBI Gene: 23379ENSG00000164151UniProt: Q9Y2F5

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]

456
ClinVar variants
113
Pathogenic / LP
1.00
pLI score· haploinsufficient
0
Active trials
Clinical Summary— ICE1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
113 Pathogenic / Likely Pathogenic· 299 VUS of 456 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.16LOEUF
pLI 1.000
Z-score 7.57
OE 0.09 (0.05–0.16)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.73Z-score
OE missense 0.94 (0.89–0.99)
1069 obs / 1138.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.09 (0.05–0.16)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.94 (0.89–0.99)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.95
0≤1.21.6
LoF obs/exp: 7 / 80.2Missense obs/exp: 1069 / 1138.2Syn Z: 0.78

ClinVar Variant Classifications

456 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic112
Likely Pathogenic1
VUS299
Likely Benign38
Benign6
112
Pathogenic
1
Likely Pathogenic
299
VUS
38
Likely Benign
6
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
112
0
112
Likely Pathogenic
0
0
1
0
1
VUS
0
297
2
0
299
Likely Benign
0
31
1
6
38
Benign
0
5
0
1
6
Total03331167456

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ICE1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Over-expression of the ICE1 gene in transgenic rice improves cold tolerance.
Kanagatov Z et al.·Braz J Biol
2025
Inducer of CBF Expression1 (ICE1) Interacts With WRKY46 to Modulate Salicylic Acid-Induced Leaf Senescence in Arabidopsis.
Yang Y et al.·Plant Cell Environ
2025
ICE1 (Inducer of CBF Expression 1) Is Essential for the Jasmonate-Regulated Development of Stamen in Arabidopsis thaliana.
Li Y et al.·Plant Cell Environ
2025
Phosphorylation-dependent activation of the bHLH transcription factor ICE1/SCRM promotes polarization of the Arabidopsis zygote.
Chen H et al.·New Phytol
2025🔓 Open Access
MYB Transcription Factor CDC5 Activates CBF3 Expression to Positively Regulate Freezing Tolerance via Cooperating With ICE1 and Histone Modification in Arabidopsis.
Xin X et al.·Plant Cell Environ
2025
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools