ICE2

interactor of little elongation complex ELL subunit 2

Basic information

Region (hg38): 15:60419609-60479160

Previous symbols: [ "NARG2" ]

Links

ENSG00000128915 ∙ NCBI:79664 ∙ OMIM:610835 ∙ HGNC:29885 ∙ Uniprot:Q659A1 ∙ 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 ICE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICE2 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				3	3	6
missense			70	3	2	75
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			1			1
Total	0	0	73	6	5

Variants in ICE2

This is a list of pathogenic ClinVar variants found in the ICE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-60423660-C-T		not specified	Uncertain significance (Jan 26, 2022)
15-60423698-C-G		not specified	Uncertain significance (Feb 19, 2025)
15-60423709-T-C		ICE2-related disorder	Likely benign (Feb 26, 2019)
15-60423762-T-A		not specified	Uncertain significance (Feb 05, 2024)
15-60428487-T-C		not specified	Uncertain significance (Sep 22, 2021)
15-60428499-T-C		not specified	Uncertain significance (Feb 26, 2025)
15-60428503-G-A		not specified	Uncertain significance (Mar 01, 2023)
15-60428598-G-A		ICE2-related disorder	Uncertain significance (May 31, 2024)
15-60428620-A-C			Likely benign (Sep 01, 2022)
15-60428673-G-T		not specified	Uncertain significance (Mar 01, 2024)
15-60431940-A-C		not specified	Uncertain significance (Jun 16, 2024)
15-60431952-A-G		not specified	Uncertain significance (Oct 26, 2021)
15-60431956-G-T		not specified	Uncertain significance (Sep 16, 2021)
15-60431994-A-G		ICE2-related disorder	Likely benign (Jun 28, 2019)
15-60436207-A-C		not specified	Uncertain significance (Feb 22, 2025)
15-60442445-A-G		not specified	Uncertain significance (Jul 10, 2024)
15-60442463-C-T		not specified	Uncertain significance (Mar 11, 2025)
15-60442498-A-G			Benign (Aug 05, 2019)
15-60442541-A-G		not specified	Uncertain significance (May 09, 2024)
15-60448009-C-G		not specified	Uncertain significance (May 05, 2022)
15-60448031-C-T		not specified	Uncertain significance (Feb 07, 2025)
15-60448032-G-T		not specified	Uncertain significance (Dec 11, 2023)
15-60448052-T-G		not specified	Uncertain significance (Sep 02, 2024)
15-60448884-A-C		not specified	Uncertain significance (Oct 13, 2023)
15-60448888-C-T		ICE2-related disorder	Likely benign (Mar 14, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICE2	protein_coding	protein_coding	ENST00000261520	15	59552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.32e-13	0.979	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.906	554	497	1.11	0.0000245	6409
Missense in Polyphen		165	162.84	1.0133		2273
Synonymous	-0.672	187	176	1.06	0.00000887	1845
Loss of Function	2.44	28	45.8	0.612	0.00000246	630

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000622	0.000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.000559	0.000544
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000349	0.000343
Middle Eastern	0.000559	0.000544
South Asian	0.000307	0.000294
Other	0.000164	0.000163

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. {ECO:0000269|PubMed:23932780}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• rvis_EVS: -0.82
• rvis_percentile_EVS: 12.01

Haploinsufficiency Scores

• pHI: 0.711
• hipred: N
• hipred_score: 0.331
• ghis: 0.656

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Ice2

Gene ontology

• Biological process: snRNA transcription by RNA polymerase II;snRNA transcription by RNA polymerase III;positive regulation of transcription by RNA polymerase III
• Cellular component: nucleoplasm;cytosol;transcription elongation factor complex;Cajal body;nuclear body;transcriptionally active chromatin;histone locus body
• Molecular function: protein binding