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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	1	6
missense			114	16	5	135
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	114	21	6

Variants in ICE1

This is a list of pathogenic ClinVar variants found in the ICE1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-5422944-C-T		not specified	Uncertain significance (Oct 26, 2021)
5-5422968-C-G		not specified	Uncertain significance (Mar 23, 2022)
5-5436470-A-G		not specified	Uncertain significance (Nov 28, 2024)
5-5436472-A-G		not specified	Uncertain significance (Jul 20, 2021)
5-5441109-T-C			Benign (Jul 31, 2018)
5-5441118-T-A		not specified	Uncertain significance (Oct 28, 2024)
5-5441201-A-G			Benign (Jun 08, 2018)
5-5443207-G-A		not specified	Uncertain significance (Dec 19, 2023)
5-5443238-A-G		not specified	Uncertain significance (Nov 07, 2024)
5-5444315-A-G		not specified	Uncertain significance (Sep 14, 2023)
5-5447734-A-T		not specified	Uncertain significance (Jun 11, 2024)
5-5447890-A-G		not specified	Uncertain significance (Mar 20, 2024)
5-5454585-T-C		not specified	Uncertain significance (May 30, 2023)
5-5457359-C-T		not specified	Uncertain significance (Nov 24, 2024)
5-5457363-A-T		not specified	Uncertain significance (Feb 27, 2023)
5-5457419-C-T		not specified	Uncertain significance (Jan 09, 2024)
5-5457468-C-A		not specified	Uncertain significance (Jul 10, 2024)
5-5457475-T-C		not specified	Uncertain significance (Dec 06, 2024)
5-5457490-A-C		not specified	Uncertain significance (Nov 07, 2024)
5-5457575-G-T		not specified	Uncertain significance (Mar 06, 2023)
5-5457580-G-A			Benign (Dec 31, 2019)
5-5457605-A-G		not specified	Uncertain significance (Feb 06, 2023)
5-5457634-G-A		not specified	Uncertain significance (Nov 03, 2022)
5-5457644-A-G		not specified	Uncertain significance (Apr 16, 2024)
5-5457653-A-G		not specified	Likely benign (Nov 29, 2023)

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