L3MBTL4

L3MBTL histone methyl-lysine binding protein 4, the group of MicroRNA protein coding host genes|MBT domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 18:5954705-6415237

Links

ENSG00000154655 ∙ NCBI:91133 ∙ OMIM:617135 ∙ HGNC:26677 ∙ Uniprot:Q8NA19 ∙ 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 L3MBTL4 gene.

• Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the L3MBTL4 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						0
missense			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in L3MBTL4

This is a list of pathogenic ClinVar variants found in the L3MBTL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-5956225-C-T		not specified	Uncertain significance (Jan 23, 2024)
18-5956246-C-T		not specified	Uncertain significance (Apr 04, 2023)
18-5956264-G-A		not specified	Uncertain significance (Feb 27, 2023)
18-5956371-G-A		not specified	Uncertain significance (Aug 13, 2021)
18-5969473-C-A		not specified	Uncertain significance (Dec 05, 2022)
18-5969482-G-C		not specified	Uncertain significance (Feb 13, 2024)
18-5969508-G-A		not specified	Uncertain significance (Jul 14, 2022)
18-5969538-T-C		not specified	Uncertain significance (Dec 15, 2023)
18-6080904-A-G		not specified	Uncertain significance (Dec 01, 2022)
18-6093388-T-C		not specified	Uncertain significance (Aug 30, 2022)
18-6093473-C-T		not specified	Uncertain significance (May 04, 2023)
18-6138212-C-T		not specified	Uncertain significance (Jun 29, 2023)
18-6138227-T-C		not specified	Uncertain significance (Jan 18, 2023)
18-6138234-T-C		not specified	Uncertain significance (May 22, 2023)
18-6138276-G-T		not specified	Uncertain significance (Jun 09, 2022)
18-6138281-T-G		not specified	Uncertain significance (Feb 10, 2022)
18-6171871-G-C		not specified	Uncertain significance (Feb 12, 2024)
18-6213164-A-C		not specified	Uncertain significance (Dec 07, 2023)
18-6213175-C-T		not specified	Likely benign (Mar 01, 2024)
18-6213231-A-G		not specified	Uncertain significance (Mar 24, 2023)
18-6215817-T-A		not specified	Uncertain significance (Jul 14, 2023)
18-6215835-C-T		not specified	Uncertain significance (Nov 21, 2022)
18-6239781-G-A		not specified	Uncertain significance (Nov 09, 2022)
18-6239783-T-C		not specified	Uncertain significance (Feb 05, 2024)
18-6239791-C-A		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
L3MBTL4	protein_coding	protein_coding	ENST00000284898	18	460532

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.10e-11	0.976	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	320	341	0.939	0.0000186	4099
Missense in Polyphen		97	124.41	0.77968		1521
Synonymous	-0.728	133	123	1.08	0.00000713	1115
Loss of Function	2.29	23	38.3	0.600	0.00000194	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000277	0.000273
Middle Eastern	0.000327	0.000326
South Asian	0.000215	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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 (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.745
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.21

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.229
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.296

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: L3mbtl4

Gene ontology

• Biological process: chromatin organization;regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity;protein binding;zinc ion binding