MLLT1

protein-coding

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

Gene summary

Predicted to enable chromatin binding activity. Predicted to be involved in positive regulation of DNA-templated transcription. Predicted to act upstream of or within negative regulation of protein kinase activity. Located in fibrillar center and nucleoplasm. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_005934.4

Inheritance

—

ClinVar variants

P:1U:66B:3

Top phenotype

Short nose

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr19:6,210,381-6,279,975

External References & Databases

Ensembl (ENSG00000130382)

Transcript & Mutation Effects

hg38 • Region Span ~69.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MLLT1 variants in ClinVar

9 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 2

Short noseTotal: 1

Abnormal cortical gyrationTotal: 1

HypotoniaTotal: 1

Cerebral atrophyTotal: 1

Global developmental delayTotal: 1

Infantile spasmsTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005934.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense		1 clinvar	62 clinvar	1 clinvar	1 clinvar	65
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	66	2	1	70

Highest pathogenic variant AF is 0.000048343132

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005934.4	RefSeq	NP_005925.2	12	MANE Select
ENST00000252674.9	Ensembl	ENSP00000252674.6	12	MANE Select
ENST00000585588.2	Ensembl	ENSP00000519594.1	6	Standard
ENST00000585588.3	Ensembl	ENSP00000519594.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding

Cellular Component

fibrillar center
nucleus
nucleoplasm
cytosol
transcription elongation factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252674
Coding exons: 12
Length: 66994
Individuals with no LoFs: 125669
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125673
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.69	197	336	0.587	0.0000225	3642
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.307

Intolerance Scores

LoFtool: 0.0111
RVIS EVS: -0.62
RVIS percentile EVS: 17.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.991

Gene Damage Prediction

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