KMT2A gene page:

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Variant policy

To annotate a new variant, you need to fill in the form with the HGVS 'c.' nomenclature. By default, the canonical isoform is selected.

If your gene of interest has several isoforms in MobiDetails, please consider to use the canonical to create your variant. If you select an alternative isoform, MobiDetails will in addition try to annotate the variant on the canonical isoform. Both annotations may be available.

In the 'Get variants' tab, variants are shown attached to their isoform.



General features Get variants

KMT2A

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Run a variant (NM_001197104.2) Choose an isoform

Running a variant means mainly generating HGVS nomenclatures via VariantValidator and creating the entry in the database. Then the variant is available forever in MobiDetails.



HGNC previous symbols ; aliases: MLL;TRX1,HRX,ALL-1,HTRX1,CXXC7,MLL1A

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Choose your destination:
  • gnomADv2 / gnomADv3 browser
  • NCBI gene
  • OMIM
  • PubMatcher
  • UCSC (hg19) / UCSC (hg38)
  • Searching for PanelApp entity...
  • OncoKB
  • MD Gene page
Gene info table:
Chr Strand Gene name Genomic Accession # Synonymous
obs/exp* (CI)		 Missense
obs/exp* (CI)		 Loss of function
obs/exp* (CI)		 OncoKB***
is oncogene?		 OncoKB***
is tumor suppressor?
11 + lysine methyltransferase 2A NG_027813.1 0.90
(0.84-0.96)		 0.61
(0.59-0.64)		 0.03
(0.01-0.07) 		No Yes


SpliceAI-visual pre-computed raw scores for KMT2A:





Transcript available for annotation in MobiDetails:



Transcript info table:
RefSeq transcript** Ensembl transcript Number of exons RefSeq protein Uniprot ID
NM_001197104.1
RefSeqSelect
ENST00000534358 36 NP_001184033.1 Q03164
NM_001197104.2
MD canonical
RefSeqSelect
MANESelect
ENST00000534358 36 NP_001184033.1 Q03164
NM_005933.3 ENST00000389506 36 NP_005924.2 Q03164
NM_005933.4 ENST00000389506 36 NP_005924.2 Q03164


*In gnomAD, the previous pLi, pRec and pNull scores have been replaced by the more accurate observed/expected scores.
Synonymous variants, nsSNVs (missense) and Loss of functions variants are reported for each gene, and compared with the expected numbers based on size and compositon of the gene. A Confidence Interval is given to better appreciate the value and if needed a threshold is defined: a class of variants is considered under constraint if the upper bound of the CI is < 0.35. See 'Gene constraint' explanations in gnomAD browser for more details.
**If the MD canonical transcript does not match the RefSeqSelect or MANESelect transcript and that there is no obvious reason to it, feel free to contact us in order to check and possibly change the MD canonical transcript. More information on the MANE project here.
***Version of the OncoKB cancer gene list available at the about page.