ICE2
Basic information
Region (hg38): 15:60419608-60479160
Previous symbols: [ "NARG2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (36 variants)
- not provided (10 variants)
- ICE2-related condition (2 variants)
- not specified (1 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.
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 | 6 | |||||
missense | 36 | 41 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 37 | 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) | ||
15-60423709-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) | ||
15-60428503-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
15-60428620-A-C | Likely benign (Sep 01, 2022) | |||
15-60428673-G-T | not specified | Uncertain significance (Mar 01, 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) | ||
15-60442498-A-G | Benign (Aug 05, 2019) | |||
15-60448009-C-G | not specified | Uncertain significance (May 05, 2022) | ||
15-60448032-G-T | not specified | Uncertain significance (Dec 11, 2023) | ||
15-60448884-A-C | not specified | Uncertain significance (Oct 13, 2023) | ||
15-60448888-C-T | ICE2-related disorder | Likely benign (Mar 14, 2019) | ||
15-60448913-C-T | not specified | Uncertain significance (Mar 02, 2023) | ||
15-60448952-T-C | not specified | Uncertain significance (Dec 28, 2023) | ||
15-60449034-C-G | not specified | Uncertain significance (May 05, 2022) | ||
15-60449034-C-T | not specified | Uncertain significance (May 31, 2023) | ||
15-60449064-T-C | not specified | Uncertain significance (Dec 28, 2022) | ||
15-60449106-T-C | not specified | Uncertain significance (Jul 14, 2023) | ||
15-60449132-T-C | not specified | Uncertain significance (Aug 02, 2022) | ||
15-60449216-C-T | not specified | Uncertain significance (Aug 08, 2022) | ||
15-60449225-T-G | not specified | Uncertain significance (Oct 03, 2022) | ||
15-60449236-A-C | not specified | Uncertain significance (Aug 08, 2023) |
GnomAD
Source:
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:
- 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
- loftool
- 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_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Ice2
- Phenotype
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