ICE1

Chr 5

interactor of little elongation complex ELL subunit 1

Also known as: KIAA0947

NCBI Gene: 23379 ENSG00000164151 OMIM: 617958

ICE1 encodes a scaffold protein that is essential for the little elongation complex (LEC), which regulates small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III. The gene is extremely intolerant to loss-of-function variants (pLI >0.99, LOEUF 0.164), suggesting mutations would likely cause severe developmental disorders, though specific associated diseases have not yet been reported in the literature. Any pathogenic variants would be expected to follow an autosomal dominant inheritance pattern given the high constraint scores.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.16

Clinical Summary— ICE1

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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.

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

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?

0.73Z-score

OE missense 0.94 (0.89–0.99)

1069 obs / 1138.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.09 (0.05–0.16)

0≤0.351.4

Missense OE?0.94 (0.89–0.99)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 7 / 80.2Missense obs/exp: 1069 / 1138.2Syn Z: 0.78

This gene — mechanism propensity

0.4488th %ile

GOF

0.3094th %ile

LOF

0.65top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.16

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.