MLLT10

MLLT10 histone lysine methyltransferase DOT1L cofactor, the group of PHD finger proteins

Basic information

Region (hg38): 10:21524646-21743630

Links

ENSG00000078403

∙ NCBI:8028 ∙ OMIM:602409 ∙ HGNC:16063 ∙ Uniprot:P55197 ∙ 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 MLLT10 gene.

not_specified (94 variants)
MLLT10-related_disorder (11 variants)
not_provided (5 variants)
Acute_myeloid_leukemia (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLLT10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001195626.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	9 clinvar	1 clinvar	13
missense			97 clinvar	4 clinvar		101
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	103	13	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLLT10	protein_coding	protein_coding	ENST00000307729	22	209466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000294	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	447	553	0.809	0.0000267	6902
Missense in Polyphen		109	190.46	0.57229		2405
Synonymous	-1.19	218	197	1.11	0.00000949	2105
Loss of Function	6.43	5	57.7	0.0867	0.00000292	698

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000889	0.0000889
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000712	0.0000703
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000986	0.0000653
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probably involved in transcriptional regulation. In vitro or as fusion protein with KMT2A/MLL1 has transactivation activity. Binds to cruciform DNA. In cells, binding to unmodified histone H3 regulates DOT1L functions including histone H3 'Lys-79' dimethylation (H3K79me2) and gene activation (PubMed:26439302). {ECO:0000269|PubMed:17868029, ECO:0000269|PubMed:26439302}.;
Disease: DISEASE: Note=A chromosomal aberration involving MLLT10 is associated with diffuse histiocytic lymphomas. Translocation t(10;11)(p13;q14) with PICALM.;

Recessive Scores

pRec: 0.177

Intolerance Scores

loftool: 0.336
rvis_EVS: -1.28
rvis_percentile_EVS: 5.13

Haploinsufficiency Scores

pHI: 0.671
hipred: Y
hipred_score: 0.792
ghis: 0.648

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mllt10
Phenotype: cellular phenotype;

Zebrafish Information Network

Gene name: mllt10
Affected structure: intestinal villus
Phenotype tag: abnormal
Phenotype quality: decreased length

Gene ontology

Biological process: positive regulation of transcription by RNA polymerase II
Cellular component: nucleus;nucleoplasm;cytosol;protein-containing complex
Molecular function: DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding;nucleosome binding;histone binding;metal ion binding