KMT2C lysine methyltransferase 2C [Homo sapiens (human)] - Gene

Summary

Official Symbol: KMT2Cprovided by HGNC
Official Full Name: lysine methyltransferase 2Cprovided by HGNC
Primary source: HGNC:HGNC:13726
See related: Ensembl:ENSG00000055609 MIM:606833; AllianceGenome:HGNC:13726
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HALR; MLL3; KLEFS2
Summary: This gene is a member of the myeloid/lymphoid or mixed-lineage leukemia (MLL) family and encodes a nuclear protein with an AT hook DNA-binding domain, a DHHC-type zinc finger, six PHD-type zinc fingers, a SET domain, a post-SET domain and a RING-type zinc finger. This protein is a member of the ASC-2/NCOA6 complex (ASCOM), which possesses histone methylation activity and is involved in transcriptional coactivation. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 8.7), bone marrow (RPKM 8.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q36.1

Exon count:: 59

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (152134925..152436003, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (153307815..153608900, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (151832010..152133088, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The modification role and tumor association with a methyltransferase: KMT2C.
Title: The modification role and tumor association with a methyltransferase: KMT2C.
Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes.
Title: Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes.
A novel 11 base pair deletion in KMT2C resulting in Kleefstra syndrome 2.
Title: A novel 11 base pair deletion in KMT2C resulting in Kleefstra syndrome 2.
Association of KMT2C/D loss-of-function variants with response to immune checkpoint blockades in colorectal cancer.
Title: Association of KMT2C/D loss-of-function variants with response to immune checkpoint blockades in colorectal cancer.
Mutations in epigenetic regulator KMT2C detected by liquid biopsy are associated with worse survival in prostate cancer patients.
Title: Mutations in epigenetic regulator KMT2C detected by liquid biopsy are associated with worse survival in prostate cancer patients.
MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer.
Title: MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer.
Association of MLL3 and TGF-beta signaling gene polymorphisms with the susceptibility and prognostic outcomes of Stanford type B aortic dissection : MLL3 with TGF-beta signal pathway association with Stanford type B AD.
Title: Association of MLL3 and TGF-β signaling gene polymorphisms with the susceptibility and prognostic outcomes of Stanford type B aortic dissection : MLL3 with TGF-β signal pathway association with Stanford type B AD.
MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state.
Title: MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state.
KMT2C Induced by FABP5P3 Aggravates Keratinocyte Hyperproliferation and Psoriasiform Skin Inflammation by Upregulating the Transcription of PIK3R3.
Title: KMT2C Induced by FABP5P3 Aggravates Keratinocyte Hyperproliferation and Psoriasiform Skin Inflammation by Upregulating the Transcription of PIK3R3.
Histone methyltransferase KMT2C plays an oncogenic role in prostate cancer.
Title: Histone methyltransferase KMT2C plays an oncogenic role in prostate cancer.

Submit: New GeneRIF Correction See all GeneRIFs (72)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Kleefstra syndrome 2 MedGen: C4540395 OMIM: 617768 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-01-24) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2018-01-24) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69864 (e-PCR)
- UniSTS:79366

RH46397 (e-PCR)
- UniSTS:76040

D7S2222 (e-PCR)
- UniSTS:45320

GDB:434012 (e-PCR)
- UniSTS:157204

L17705 (e-PCR)
- UniSTS:66091

AFMa153wd9 (e-PCR)
- UniSTS:17216

SHGC-105317 (e-PCR)
- UniSTS:169289

RH118851 (e-PCR)
- UniSTS:138832

L17709 (e-PCR)
- UniSTS:42599

D7S3200 (e-PCR)
- UniSTS:229482

RH16362 (e-PCR)
- UniSTS:55914

D7S3202 (e-PCR)
- UniSTS:229484

D7S3203 (e-PCR)
- UniSTS:229485

D7S3204 (e-PCR)
- UniSTS:229486

D7S3205 (e-PCR)
- UniSTS:229487

SGC34800 (e-PCR)
- UniSTS:16240

D7S3206 (e-PCR)
- UniSTS:229488

RH104360 (e-PCR)
- UniSTS:98685

SHGC-35156 (e-PCR)
- UniSTS:42643

L17877 (e-PCR)
- UniSTS:61334

G18004 (e-PCR)
- UniSTS:38816

GDB:1318392 (e-PCR)
- UniSTS:46249

RH16464 (e-PCR)
- UniSTS:4525

GDB:1318126 (e-PCR)
- UniSTS:8894

GDB:4585181 (e-PCR)
- UniSTS:59346

RH45284 (e-PCR)
- UniSTS:68307

D3S1673 (e-PCR)
- UniSTS:148450

WI-17647 (e-PCR)
- UniSTS:67575

Clone Names

FLJ12625, FLJ38309, KIAA1506, MGC119851, MGC119852, MGC119853, DKFZp686C08112

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables acyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to electrical stimulus	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of MLL3/4 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of MLL3/4 complex	IDA Inferred from Direct Assay more info	PubMed
part_of MLL3/4 complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
part_of histone methyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase 2C

Names: ALR-like protein; histone-lysine N-methyltransferase MLL3; histone-lysine N-methyltransferase, H3 lysine-4 specific; homologous to ALR protein; lysine (K)-specific methyltransferase 2C; myeloid/lymphoid or mixed-lineage leukemia protein 3

NP_733751.2

EC 2.1.1.364

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033948.1 RefSeqGene

Range

5003..306081

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_170606.3 → NP_733751.2 histone-lysine N-methyltransferase 2C

See identical proteins and their annotated locations for NP_733751.2

Status: REVIEWED

Source sequence(s)

AF264750, AK025911, AY024361, BP281562, BU623509, BU685177, CD513584

Consensus CDS

CCDS5931.1

UniProtKB/Swiss-Prot

Q8NC02, Q8NDF6, Q8NEZ4, Q9H9P4, Q9NR13, Q9P222, Q9UDR7

UniProtKB/TrEMBL

A0A7P0TAI3

Related

ENSP00000262189.6, ENST00000262189.11

Conserved Domains (17) summary

smart00317
Location:4772 → 4893

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

smart00508
Location:4895 → 4911

PostSET; Cysteine-rich motif following a subset of SET domains

COG2940
Location:4725 → 4911

SET; SET domain-containing protein (function unknown) [General function prediction only]

sd00025
Location:1084 → 1106

zf-RanBP2; RanBP2-type Zn finger [structural motif]

cd15509
Location:343 → 388

PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)

cd15511
Location:466 → 517

PHD3_KMT2C; PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C)

cd15513
Location:1009 → 1055

PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D

cd15594
Location:390 → 435

PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)

cd15596
Location:952 → 1008

PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)

cd15600
Location:1086 → 1136

PHD6_KMT2C; PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C)

cd15696
Location:247 → 330

ePHD1_KMT2C; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C)

cd15697
Location:4402 → 4506

ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)

pfam05964
Location:4552 → 4602

FYRN; F/Y-rich N-terminus

pfam05965
Location:4608 → 4689

FYRC; F/Y rich C-terminus

pfam11176
Location:1692 → 1775

DUF2962; Protein of unknown function (DUF2962)

pfam15233
Location:3181 → 3270

SYCE1; Synaptonemal complex central element protein 1

cl00082
Location:1654 → 1705

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

152134925..152436003 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

153307815..153608900 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_021230.2: Suppressed sequence

Description

NM_021230.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.