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.

• not_specified (129 variants)
• ICE2-related_disorder (12 variants)
• not_provided (9 variants)
• NARG2-related_Intellectual_disability (2 variants)

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. These statistics are base on transcript: NM_000024611.6. 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				7	2	9
missense			125	8	2	135
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	127	15	4

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