L3MBTL2
Basic information
Region (hg38): 22:41205282-41231271
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the L3MBTL2 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 | |||||
missense | 50 | 52 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 51 | 2 | 3 |
Variants in L3MBTL2
This is a list of pathogenic ClinVar variants found in the L3MBTL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-41205371-G-T | not specified | Uncertain significance (Oct 27, 2021) | ||
22-41205382-T-C | not specified | Uncertain significance (Jul 26, 2022) | ||
22-41209760-A-G | not specified | Uncertain significance (Jul 09, 2021) | ||
22-41209772-G-C | Benign (Oct 29, 2020) | |||
22-41209796-G-A | not specified | Uncertain significance (Apr 25, 2023) | ||
22-41209836-A-T | not specified | Uncertain significance (Feb 17, 2024) | ||
22-41209888-A-G | not specified | Uncertain significance (Mar 08, 2024) | ||
22-41209901-C-A | not specified | Uncertain significance (Feb 27, 2023) | ||
22-41209903-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
22-41216260-A-T | not specified | Uncertain significance (Nov 08, 2022) | ||
22-41217159-A-G | not specified | Uncertain significance (Jun 07, 2023) | ||
22-41217177-C-T | not specified | Uncertain significance (Oct 26, 2022) | ||
22-41219445-T-A | not specified | Uncertain significance (Jan 04, 2022) | ||
22-41219470-G-C | not specified | Uncertain significance (Mar 01, 2023) | ||
22-41219515-G-A | not specified | Uncertain significance (Sep 13, 2023) | ||
22-41219521-G-A | not specified | Uncertain significance (Jun 28, 2022) | ||
22-41220774-C-T | Benign (Jun 27, 2018) | |||
22-41220782-A-T | not specified | Uncertain significance (Nov 06, 2023) | ||
22-41220789-C-G | not specified | Uncertain significance (Oct 28, 2024) | ||
22-41220794-G-A | not specified | Uncertain significance (Dec 09, 2024) | ||
22-41220823-A-C | not specified | Uncertain significance (May 25, 2022) | ||
22-41221219-G-A | not specified | Uncertain significance (Apr 25, 2023) | ||
22-41221244-G-A | not specified | Uncertain significance (Jun 05, 2023) | ||
22-41221246-C-G | not specified | Uncertain significance (Aug 12, 2021) | ||
22-41221270-G-A | not specified | Uncertain significance (May 25, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
L3MBTL2 | protein_coding | protein_coding | ENST00000216237 | 17 | 26067 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.03e-8 | 0.999 | 125708 | 0 | 40 | 125748 | 0.000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.92 | 322 | 435 | 0.740 | 0.0000263 | 4639 |
Missense in Polyphen | 75 | 125.11 | 0.59946 | 1347 | ||
Synonymous | 0.137 | 174 | 176 | 0.987 | 0.0000119 | 1338 |
Loss of Function | 2.99 | 20 | 40.6 | 0.493 | 0.00000227 | 430 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000668 | 0.000666 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.0000973 | 0.0000924 |
European (Non-Finnish) | 0.000167 | 0.000158 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.0000981 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Putative Polycomb group (PcG) protein. PcG proteins maintain the transcriptionally repressive state of genes, probably via a modification of chromatin, rendering it heritably changed in its expressibility. Its association with a chromatin-remodeling complex suggests that it may contribute to prevent expression of genes that trigger the cell into mitosis. Binds to monomethylated and dimethylated 'Lys-20' on histone H4. Binds histone H3 peptides that are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. {ECO:0000269|PubMed:19233876}.;
- Pathway
- Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation
(Consensus)
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.641
- rvis_EVS
- -1.17
- rvis_percentile_EVS
- 6.03
Haploinsufficiency Scores
- pHI
- 0.302
- hipred
- Y
- hipred_score
- 0.603
- ghis
- 0.615
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.591
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- L3mbtl2
- Phenotype
- skeleton phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype;
Gene ontology
- Biological process
- chromatin organization;regulation of transcription, DNA-templated;negative regulation of G0 to G1 transition
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- protein binding;zinc ion binding;methylated histone binding;histone binding