MLLT1

MLLT1 super elongation complex subunit, the group of YEATS domain containing|Super elongation complex

Basic information

Region (hg38): 19:6210381-6279975

Links

ENSG00000130382 ∙ NCBI:4298 ∙ OMIM:159556 ∙ HGNC:7134 ∙ Uniprot:Q03111 ∙ 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 MLLT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLLT1 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			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	1

Variants in MLLT1

This is a list of pathogenic ClinVar variants found in the MLLT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6213079-C-T			Uncertain significance (Jan 01, 2023)
19-6213092-C-T		not specified	Uncertain significance (May 04, 2023)
19-6213745-T-C		not specified	Uncertain significance (Nov 03, 2023)
19-6213779-G-A		not specified	Uncertain significance (Sep 29, 2023)
19-6213787-C-T		7 conditions	Likely pathogenic (Jan 10, 2016)
19-6213982-C-T		not specified	Uncertain significance (Feb 17, 2023)
19-6214001-C-T		not specified	Uncertain significance (Jul 13, 2021)
19-6222128-T-G		not specified	Uncertain significance (Nov 09, 2023)
19-6222174-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-6222257-G-A		not specified	Uncertain significance (Feb 05, 2024)
19-6222293-C-G		not specified	Uncertain significance (Jan 04, 2022)
19-6222306-G-A		not specified	Uncertain significance (Jul 12, 2023)
19-6222345-T-C		not specified	Uncertain significance (Aug 21, 2023)
19-6222363-C-T		not specified	Uncertain significance (Mar 19, 2024)
19-6222371-G-A		not specified	Uncertain significance (Sep 25, 2023)
19-6222437-C-A		not specified	Uncertain significance (Apr 09, 2024)
19-6222542-G-A			Benign (Jul 19, 2018)
19-6222677-T-C		not specified	Likely benign (Dec 28, 2023)
19-6227054-C-T		not specified	Uncertain significance (Jun 13, 2023)
19-6227074-G-T		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLLT1	protein_coding	protein_coding	ENST00000252674	12	66994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0133	125669	0	4	125673	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.69	197	336	0.587	0.0000225	3642
Missense in Polyphen		31	83.407	0.37167		790
Synonymous	-0.452	157	150	1.05	0.0000111	1073
Loss of Function	3.94	2	21.9	0.0914	9.26e-7	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000570	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000270	0.0000264
Middle Eastern	0.0000570	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. {ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948}.
• Disease: DISEASE: Note=A chromosomal aberration involving MLLT1 is associated with acute leukemias. Translocation t(11;19)(q23;p13.3) with KMT2A/MLL1. The result is a rogue activator protein.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;RNA Polymerase II Transcription Elongation (Consensus)

Recessive Scores

• pRec: 0.307

Intolerance Scores

• loftool: 0.0111
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.206
• hipred: Y
• hipred_score: 0.825
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mllt1
• 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); normal phenotype; hematopoietic system phenotype; neoplasm; liver/biliary system phenotype; immune system phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;negative regulation of protein kinase activity
• Cellular component: fibrillar center;nucleus;nucleoplasm;cytosol;transcription elongation factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding