ICE1

interactor of little elongation complex ELL subunit 1

Basic information

Region (hg38): 5:5420664-5490220

Previous symbols: [ "KIAA0947" ]

Links

ENSG00000164151 ∙ NCBI:23379 ∙ OMIM:617958 ∙ HGNC:29154 ∙ Uniprot:Q9Y2F5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ICE1 gene.

• not_specified (285 variants)
• not_provided (11 variants)
• ICE1-related_disorder (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICE1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015325.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6	1	7
missense			260	28	4	292
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	260	34	5

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICE1	protein_coding	protein_coding	ENST00000296564	19	69571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.74e-8	124614	0	31	124645	0.000124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.729	1069	1.14e+3	0.939	0.0000577	14783
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000298	0.000297
Ashkenazi Jewish	0.000313	0.000298
East Asian	0.000285	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000121	0.000115
Middle Eastern	0.000285	0.000278
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.58

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.314
• ghis: 0.569

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Ice1

Zebrafish Information Network

• Gene name: ice1
• Affected structure: liver
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• 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
• Cellular component: nucleoplasm;transcription elongation factor complex;Cajal body;nuclear body;transcriptionally active chromatin;histone locus body
• Molecular function: protein binding;protein homodimerization activity