MALAT1

Chr 11

metastasis associated lung adenocarcinoma transcript 1

Also known as: HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, miPEP-52

NCBI Gene: 378938 ENSG00000251562 OMIM: 607924

MALAT1 encodes a long non-coding RNA that forms nuclear scaffolds for ribonucleoprotein complexes and regulates transcription of genes involved in cell cycle regulation, cancer metastasis, and cell migration. While upregulated in various cancers, pathogenic germline variants in MALAT1 have not been definitively associated with Mendelian pediatric neurological disorders. The gene is primarily studied in the context of oncology rather than inherited neurogenetic conditions.

OMIM ResearchSummary from RefSeq

This gene produces a precursor transcript from which a long non-coding RNA is derived by RNase P cleavage of a tRNA-like small ncRNA (known as mascRNA) from its 3' end. The resultant mature transcript lacks a canonical poly(A) tail but is instead stabilized by a 3' triple helical structure. This transcript is retained in the nucleus where it is thought to form molecular scaffolds for ribonucleoprotein complexes. It may act as a transcriptional regulator for numerous genes, including some genes involved in cancer metastasis and cell migration, and it is involved in cell cycle regulation. Its upregulation in multiple cancerous tissues has been associated with the proliferation and metastasis of tumor cells. [provided by RefSeq, Mar 2015]

OMIM ResearchGenerating clinical summary…

Active trials

490

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

—

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in MALAT1?

gnomAD v4 · ~183k individuals · PASS only

Rare means allele frequency under

Rare missense

none observed

0 rare PASS variants

Rare truncating (LoF)

1 in 830

51 rare PASS variants

Rare synonymous (reference)

none observed

0 rare PASS variants

Rare missense and truncating variants are carried at similar rates in MALAT1; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~96k	none seen	1 in 1,900
South Asian	~33k	none seen	1 in 340
African / African American	~21k	none seen	1 in 3,400
Admixed American	~18k	none seen	1 in 640
European (Finnish)	~8,468	none seen	≈ 1 in 4,200
Remaining (unassigned)	~8,305	none seen	1 in 710
East Asian	~6,586	none seen	≈ 1 in 1,800
Ashkenazi Jewish	~5,872	none seen	≈ 1 in 5,900
Middle Eastern	~1,426	none seen	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.