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.

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.

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				5	2	7
missense			45	3		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	1	5
non coding				1	2	3
Total	0	0	45	9	4

Variants in MLLT10

This is a list of pathogenic ClinVar variants found in the MLLT10 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-21534690-C-T		not specified	Uncertain significance (Dec 02, 2021)
10-21534743-C-T			Likely benign (Oct 01, 2022)
10-21538867-G-A		MLLT10-related disorder	Benign (Sep 24, 2019)
10-21556866-A-T		MLLT10-related disorder	Benign (May 22, 2019)
10-21586325-C-G		not specified	Uncertain significance (Feb 02, 2022)
10-21595332-T-C		MLLT10-related disorder	Likely benign (Jun 25, 2019)
10-21612326-CTT-C		MLLT10-related disorder	Benign (Jul 15, 2019)
10-21612397-G-C		not specified	Uncertain significance (Jan 27, 2022)
10-21614831-C-T		not specified	Likely benign (May 30, 2023)
10-21651678-T-C		MLLT10-related disorder	Likely benign (Apr 09, 2019)
10-21670478-A-G		not specified	Uncertain significance (Feb 28, 2024)
10-21670545-T-C		not specified	Uncertain significance (Aug 05, 2023)
10-21670584-A-G		not specified	Uncertain significance (Apr 15, 2024)
10-21670602-G-A		not specified	Uncertain significance (Aug 26, 2022)
10-21673318-CTTTTT-C		MLLT10-related disorder	Likely benign (Apr 09, 2019)
10-21673392-G-T		not specified	Uncertain significance (Feb 02, 2022)
10-21673395-G-A		not specified	Uncertain significance (Jan 16, 2024)
10-21673438-A-G			Likely benign (Dec 01, 2023)
10-21673498-T-C		MLLT10-related disorder	Likely benign (Jul 15, 2019)
10-21673524-G-C		Acute myeloid leukemia	Uncertain significance (Mar 22, 2018)
10-21673526-G-A		not specified	Uncertain significance (Mar 07, 2023)
10-21673616-T-G		not specified	Uncertain significance (Jan 09, 2024)
10-21673634-C-T		not specified	Uncertain significance (Oct 03, 2022)
10-21673641-C-T		not specified	Uncertain significance (Dec 15, 2023)
10-21673724-C-A		not specified	Uncertain significance (Apr 13, 2023)

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