VCPKMT (valosin containing protein lysine methyltransferase) - Rat Genome Database

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Gene: VCPKMT (valosin containing protein lysine methyltransferase) Homo sapiens
Analyze
Symbol: VCPKMT
Name: valosin containing protein lysine methyltransferase
RGD ID: 1314724
HGNC Page HGNC:20352
Description: Enables ATPase binding activity and protein-lysine N-methyltransferase activity. Predicted to be involved in chromatin remodeling and methylation. Located in cytosol. Part of protein-containing complex.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C14orf138; FLJ13920; hypothetical protein LOC79609; methyltransferase like 21D; methyltransferase-like protein 21D; METTL21D; protein-lysine methyltransferase METTL21D; valosin containing protein lysine (K) methyltransferase; valosin-containing protein lysine methyltransferase; VCP lysine methyltransferase; VCP-KMT
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC100129497  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381450,102,716 - 50,116,572 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1450,108,632 - 50,116,600 (-)EnsemblGRCh38hg38GRCh38
GRCh371450,575,355 - 50,583,290 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361449,645,100 - 49,653,047 (-)NCBINCBI36Build 36hg18NCBI36
Build 341449,645,105 - 49,653,047NCBI
Celera1430,442,491 - 30,450,433 (-)NCBICelera
Cytogenetic Map14q21.3NCBI
HuRef1430,700,814 - 30,708,767 (-)NCBIHuRef
CHM1_11450,514,037 - 50,522,000 (-)NCBICHM1_1
T2T-CHM13v2.01444,309,674 - 44,322,811 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IDA,IEA)
cytosol  (IBA,IDA,IEA,TAS)
protein-containing complex  (IBA,IDA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:15489334   PMID:21873635   PMID:22948820   PMID:23349634   PMID:26186194   PMID:27432908   PMID:28514442   PMID:29599191   PMID:32296183   PMID:33961781  
PMID:35831314   PMID:36656859  


Genomics

Comparative Map Data
VCPKMT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381450,102,716 - 50,116,572 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1450,108,632 - 50,116,600 (-)EnsemblGRCh38hg38GRCh38
GRCh371450,575,355 - 50,583,290 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361449,645,100 - 49,653,047 (-)NCBINCBI36Build 36hg18NCBI36
Build 341449,645,105 - 49,653,047NCBI
Celera1430,442,491 - 30,450,433 (-)NCBICelera
Cytogenetic Map14q21.3NCBI
HuRef1430,700,814 - 30,708,767 (-)NCBIHuRef
CHM1_11450,514,037 - 50,522,000 (-)NCBICHM1_1
T2T-CHM13v2.01444,309,674 - 44,322,811 (-)NCBIT2T-CHM13v2.0
Vcpkmt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391269,623,504 - 69,629,883 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1269,624,402 - 69,629,884 (-)EnsemblGRCm39 Ensembl
GRCm381269,576,735 - 69,583,017 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1269,577,628 - 69,583,110 (-)EnsemblGRCm38mm10GRCm38
MGSCv371270,678,615 - 70,684,015 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361270,498,281 - 70,501,620 (-)NCBIMGSCv36mm8
Celera1270,666,463 - 70,671,887 (-)NCBICelera
Cytogenetic Map12C2NCBI
cM Map1228.92NCBI
Vcpkmt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8693,772,558 - 93,778,400 (-)NCBIGRCr8
mRatBN7.2688,036,485 - 88,042,151 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl688,036,494 - 88,042,000 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0691,880,342 - 91,884,336 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06101,330,561 - 101,336,079 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4691,602,980 - 91,610,509 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera686,533,202 - 86,537,196 (-)NCBICelera
Cytogenetic Map6q24NCBI
Vcpkmt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540912,622,259 - 12,632,246 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540912,622,259 - 12,632,246 (+)NCBIChiLan1.0ChiLan1.0
VCPKMT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21551,245,296 - 51,257,054 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11450,461,800 - 50,473,274 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01430,695,992 - 30,707,327 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11449,002,181 - 49,013,187 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1449,002,181 - 49,013,187 (-)Ensemblpanpan1.1panPan2
VCPKMT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1826,611,333 - 26,636,700 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl826,625,677 - 26,636,316 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha826,364,923 - 26,390,315 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0826,789,131 - 26,814,525 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl826,807,761 - 26,814,116 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1826,444,053 - 26,469,453 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0826,516,540 - 26,541,946 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0826,835,201 - 26,860,599 (-)NCBIUU_Cfam_GSD_1.0
Vcpkmt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405947353 - 5,484 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049401971,070 - 5,090 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004940197408 - 5,645 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCPKMT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1179,899,646 - 179,906,967 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11179,899,642 - 179,907,439 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21200,260,935 - 200,262,345 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VCPKMT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12427,173,859 - 27,182,941 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2427,173,840 - 27,182,924 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605315,504,133 - 15,512,575 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vcpkmt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473118,694,647 - 18,704,199 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473118,694,765 - 18,704,199 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VCPKMT
14 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q21.3-22.1(chr14:50091150-51777325)x3 copy number gain See cases [RCV000052059] Chr14:50091150..51777325 [GRCh38]
Chr14:50557868..52244043 [GRCh37]
Chr14:49627618..51313793 [NCBI36]
Chr14:14q21.3-22.1
uncertain significance
NM_001040662.1(VCPKMT):c.104C>T (p.Ser35Phe) single nucleotide variant Malignant melanoma [RCV000070543] Chr14:50116449 [GRCh38]
Chr14:50583167 [GRCh37]
Chr14:49652917 [NCBI36]
Chr14:14q21.3
not provided
NM_006939.2(SOS2):c.3491G>A (p.Gly1164Glu) single nucleotide variant Malignant melanoma [RCV000070544] Chr14:50118852 [GRCh38]
Chr14:50585570 [GRCh37]
Chr14:49655320 [NCBI36]
Chr14:14q21.3
not provided
NM_006939.2(SOS2):c.3490G>A (p.Gly1164Arg) single nucleotide variant Malignant melanoma [RCV000070545] Chr14:50118853 [GRCh38]
Chr14:50585571 [GRCh37]
Chr14:49655321 [NCBI36]
Chr14:14q21.3
not provided
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33
pathogenic
GRCh38/hg38 14q21.1-22.3(chr14:39196172-56714461)x3 copy number gain See cases [RCV000140717] Chr14:39196172..56714461 [GRCh38]
Chr14:39665376..57181179 [GRCh37]
Chr14:38735127..56250932 [NCBI36]
Chr14:14q21.1-22.3
likely pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33
pathogenic
L2HGDH, EX1-9DEL deletion L-2-hydroxyglutaric aciduria [RCV000001678] Chr14:50000000..50247254 [GRCh38]
Chr14:14q21.3
pathogenic
GRCh37/hg19 14q11.2-22.2(chr14:23164384-54733411)x3 copy number gain See cases [RCV000447658] Chr14:23164384..54733411 [GRCh37]
Chr14:14q11.2-22.2
pathogenic
GRCh37/hg19 14q11.2-32.33(chr14:19794561-107234280)x3 copy number gain See cases [RCV000446256] Chr14:19794561..107234280 [GRCh37]
Chr14:14q11.2-32.33
pathogenic
GRCh37/hg19 14q11.2-32.33(chr14:20511673-107285437) copy number gain See cases [RCV000512041] Chr14:20511673..107285437 [GRCh37]
Chr14:14q11.2-32.33
pathogenic
NM_024558.3(VCPKMT):c.508A>G (p.Ile170Val) single nucleotide variant Inborn genetic diseases [RCV003281583] Chr14:50114347 [GRCh38]
Chr14:50581065 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.394G>A (p.Gly132Ser) single nucleotide variant Inborn genetic diseases [RCV003304584] Chr14:50115895 [GRCh38]
Chr14:50582613 [GRCh37]
Chr14:14q21.3
uncertain significance
GRCh37/hg19 14q11.1-32.33(chr14:19000422-107289053)x3 copy number gain not provided [RCV000738412] Chr14:19000422..107289053 [GRCh37]
Chr14:14q11.1-32.33
pathogenic
GRCh37/hg19 14q11.2-32.33(chr14:19280733-107287663)x3 copy number gain not provided [RCV000738413] Chr14:19280733..107287663 [GRCh37]
Chr14:14q11.2-32.33
pathogenic
GRCh37/hg19 14q11.2-32.33(chr14:19327823-107287663)x3 copy number gain not provided [RCV000738414] Chr14:19327823..107287663 [GRCh37]
Chr14:14q11.2-32.33
pathogenic
NM_024558.3(VCPKMT):c.99T>G (p.Tyr33Ter) single nucleotide variant not provided [RCV000807596]|not specified [RCV001005055] Chr14:50116454 [GRCh38]
Chr14:50583172 [GRCh37]
Chr14:14q21.3
uncertain significance
NC_000014.8:g.(?_50092240)_(50698021_?)dup duplication Noonan syndrome 9 [RCV000799423] Chr14:49625522..50231303 [GRCh38]
Chr14:50092240..50698021 [GRCh37]
Chr14:14q21.3
uncertain significance
GRCh37/hg19 14q21.3-22.1(chr14:50317272-51627752)x3 copy number gain not provided [RCV001006632] Chr14:50317272..51627752 [GRCh37]
Chr14:14q21.3-22.1
uncertain significance
NC_000014.8:g.(21162263_36986276)_(36987308_50713602)del deletion Brain-lung-thyroid syndrome [RCV002221171] Chr14:36986276..36987308 [GRCh37]
Chr14:14q11.2-21.3
pathogenic
GRCh37/hg19 14q13.3-32.33(chr14:37671058-106985955)x2 copy number gain See cases [RCV002286356] Chr14:37671058..106985955 [GRCh37]
Chr14:14q13.3-32.33
pathogenic
NM_024558.3(VCPKMT):c.666G>C (p.Lys222Asn) single nucleotide variant Inborn genetic diseases [RCV002682189] Chr14:50112624 [GRCh38]
Chr14:50579342 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.672A>C (p.Lys224Asn) single nucleotide variant Inborn genetic diseases [RCV002779073] Chr14:50112618 [GRCh38]
Chr14:50579336 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.35C>T (p.Pro12Leu) single nucleotide variant Inborn genetic diseases [RCV002951582] Chr14:50116518 [GRCh38]
Chr14:50583236 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.605C>A (p.Pro202His) single nucleotide variant Inborn genetic diseases [RCV002822632] Chr14:50112685 [GRCh38]
Chr14:50579403 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.140T>C (p.Ile47Thr) single nucleotide variant Inborn genetic diseases [RCV002652270] Chr14:50116413 [GRCh38]
Chr14:50583131 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.209C>T (p.Ser70Leu) single nucleotide variant Inborn genetic diseases [RCV002964477] Chr14:50116344 [GRCh38]
Chr14:50583062 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.443A>G (p.Tyr148Cys) single nucleotide variant Inborn genetic diseases [RCV002898006] Chr14:50115846 [GRCh38]
Chr14:50582564 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.52C>G (p.Arg18Gly) single nucleotide variant Inborn genetic diseases [RCV003192791] Chr14:50116501 [GRCh38]
Chr14:50583219 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.283A>C (p.Thr95Pro) single nucleotide variant Inborn genetic diseases [RCV003186426] Chr14:50116163 [GRCh38]
Chr14:50582881 [GRCh37]
Chr14:14q21.3
uncertain significance
NM_024558.3(VCPKMT):c.574C>T (p.Leu192Phe) single nucleotide variant Inborn genetic diseases [RCV003361218] Chr14:50112716 [GRCh38]
Chr14:50579434 [GRCh37]
Chr14:14q21.3
uncertain significance
GRCh37/hg19 14q11.2-23.1(chr14:20511673-61826023)x3 copy number gain not provided [RCV003485022] Chr14:20511673..61826023 [GRCh37]
Chr14:14q11.2-23.1
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1145
Count of miRNA genes:476
Interacting mature miRNAs:522
Transcripts:ENST00000395859, ENST00000395860, ENST00000484763, ENST00000491402, ENST00000569518
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
D13S1686  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371450,583,882 - 50,584,030UniSTSGRCh37
Build 361449,653,632 - 49,653,780RGDNCBI36
Celera1430,451,018 - 30,451,166RGD
Cytogenetic Map14q21UniSTS
Cytogenetic Map14q21.3UniSTS
HuRef1430,709,352 - 30,709,500UniSTS
RH80099  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371450,575,386 - 50,575,630UniSTSGRCh37
GRCh37138,246,832 - 38,247,084UniSTSGRCh37
Build 36138,019,419 - 38,019,671RGDNCBI36
Celera1430,442,527 - 30,442,771UniSTS
Celera136,524,664 - 36,524,916RGD
Cytogenetic Map14q21.3UniSTS
HuRef1430,700,850 - 30,701,094UniSTS
HuRef136,364,982 - 36,365,234UniSTS
GeneMap99-GB4 RH Map1117.53UniSTS
RH65681  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37138,247,667 - 38,247,825UniSTSGRCh37
GRCh371450,576,204 - 50,576,356UniSTSGRCh37
Build 36138,020,254 - 38,020,412RGDNCBI36
Celera136,525,498 - 36,525,656RGD
Celera1430,443,345 - 30,443,497UniSTS
Cytogenetic Map14q21.3UniSTS
Cytogenetic Map1p34.3UniSTS
HuRef136,365,816 - 36,365,974UniSTS
HuRef1430,701,668 - 30,701,820UniSTS
SHGC-64140  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371450,576,093 - 50,576,311UniSTSGRCh37
Build 361449,645,843 - 49,646,061RGDNCBI36
Celera1430,443,234 - 30,443,452RGD
Cytogenetic Map14q21.3UniSTS
HuRef1430,701,557 - 30,701,775UniSTS
TNG Radiation Hybrid Map1413845.0UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 1746 1433 1079 129 1448 79 3086 722 1998 136 1329 1447 62 868 1788 3
Low 693 1555 647 495 500 386 1271 1475 1736 283 131 166 112 1 336 1000 3 2
Below cutoff 3 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001040662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_024558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_049738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_049739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005268060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017021640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017021641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024449709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047431773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054376712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054376713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054376714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001750551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001750552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_007064045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_008488895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_008488896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_943531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_943532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AK023982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK129564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL109758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AX881055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC027585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC105118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC143673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC143674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI753530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI767189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX247997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENST00000395859   ⟹   ENSP00000379200
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1450,109,537 - 50,116,600 (-)Ensembl
RefSeq Acc Id: ENST00000395860   ⟹   ENSP00000379201
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1450,108,637 - 50,116,572 (-)Ensembl
RefSeq Acc Id: ENST00000484763
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1450,108,642 - 50,116,558 (-)Ensembl
RefSeq Acc Id: ENST00000491402   ⟹   ENSP00000437113
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1450,108,633 - 50,116,600 (-)Ensembl
RefSeq Acc Id: ENST00000569518
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1450,108,632 - 50,116,477 (-)Ensembl
RefSeq Acc Id: NM_001040662   ⟹   NP_001035752
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,108,637 - 50,116,572 (-)NCBI
GRCh371450,572,967 - 50,583,626 (-)NCBI
Build 361449,645,100 - 49,653,047 (-)NCBI Archive
Celera1430,442,491 - 30,450,433 (-)RGD
HuRef1430,700,814 - 30,708,767 (-)RGD
CHM1_11450,514,037 - 50,522,000 (-)NCBI
T2T-CHM13v2.01444,314,875 - 44,322,811 (-)NCBI
Sequence:
RefSeq Acc Id: NM_024558   ⟹   NP_078834
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,108,637 - 50,116,572 (-)NCBI
GRCh371450,572,967 - 50,583,626 (-)NCBI
Build 361449,645,100 - 49,653,047 (-)NCBI Archive
Celera1430,442,491 - 30,450,433 (-)RGD
HuRef1430,700,814 - 30,708,767 (-)RGD
CHM1_11450,514,037 - 50,522,000 (-)NCBI
T2T-CHM13v2.01444,314,875 - 44,322,811 (-)NCBI
Sequence:
RefSeq Acc Id: NR_049738
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,108,637 - 50,116,572 (-)NCBI
GRCh371450,572,967 - 50,583,626 (-)NCBI
HuRef1430,700,814 - 30,708,767 (-)NCBI
CHM1_11450,514,037 - 50,522,000 (-)NCBI
T2T-CHM13v2.01444,314,875 - 44,322,811 (-)NCBI
Sequence:
RefSeq Acc Id: NR_049739
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,108,637 - 50,116,572 (-)NCBI
GRCh371450,572,967 - 50,583,626 (-)NCBI
HuRef1430,700,814 - 30,708,767 (-)NCBI
CHM1_11450,514,037 - 50,522,000 (-)NCBI
T2T-CHM13v2.01444,314,875 - 44,322,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005268060   ⟹   XP_005268117
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,108,637 - 50,116,572 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017021640   ⟹   XP_016877129
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,102,716 - 50,116,572 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047431773   ⟹   XP_047287729
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,108,637 - 50,116,572 (-)NCBI
RefSeq Acc Id: XM_054376712   ⟹   XP_054232687
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01444,314,875 - 44,322,811 (-)NCBI
RefSeq Acc Id: XM_054376713   ⟹   XP_054232688
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01444,309,674 - 44,322,811 (-)NCBI
RefSeq Acc Id: XM_054376714   ⟹   XP_054232689
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01444,314,875 - 44,322,811 (-)NCBI
RefSeq Acc Id: XR_007064045
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,112,639 - 50,116,572 (-)NCBI
RefSeq Acc Id: XR_008488895
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01444,318,874 - 44,322,811 (-)NCBI
RefSeq Acc Id: XR_008488896
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01444,318,870 - 44,322,811 (-)NCBI
RefSeq Acc Id: XR_943532
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,112,635 - 50,116,572 (-)NCBI
Sequence:
RefSeq Acc Id: NP_078834   ⟸   NM_024558
- Peptide Label: isoform a
- UniProtKB: Q2M2X3 (UniProtKB/Swiss-Prot),   B7ZLA4 (UniProtKB/Swiss-Prot),   B7ZLA3 (UniProtKB/Swiss-Prot),   Q86T12 (UniProtKB/Swiss-Prot),   Q9H867 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001035752   ⟸   NM_001040662
- Peptide Label: isoform b
- UniProtKB: Q9H867 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_005268117   ⟸   XM_005268060
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_016877129   ⟸   XM_017021640
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSP00000437113   ⟸   ENST00000491402
RefSeq Acc Id: ENSP00000379200   ⟸   ENST00000395859
RefSeq Acc Id: ENSP00000379201   ⟸   ENST00000395860
RefSeq Acc Id: XP_047287729   ⟸   XM_047431773
- Peptide Label: isoform X3
RefSeq Acc Id: XP_054232688   ⟸   XM_054376713
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054232687   ⟸   XM_054376712
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054232689   ⟸   XM_054376714
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9H867-F1-model_v2 AlphaFold Q9H867 1-229 view protein structure

Promoters
RGD ID:6791320
Promoter ID:HG_KWN:19332
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000358490,   NM_001040662,   NM_024558,   OTTHUMT00000073611,   OTTHUMT00000276876,   UC001WXN.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361449,652,831 - 49,653,331 (-)MPROMDB
RGD ID:7227541
Promoter ID:EPDNEW_H19516
Type:initiation region
Name:VCPKMT_1
Description:valosin containing protein lysine methyltransferase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,116,565 - 50,116,625EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:20352 AgrOrtholog
COSMIC VCPKMT COSMIC
Ensembl Genes ENSG00000100483 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000395859 ENTREZGENE
  ENST00000395859.2 UniProtKB/Swiss-Prot
  ENST00000395860 ENTREZGENE
  ENST00000395860.7 UniProtKB/Swiss-Prot
  ENST00000484763 ENTREZGENE
  ENST00000491402 ENTREZGENE
  ENST00000491402.5 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.150 UniProtKB/Swiss-Prot
GTEx ENSG00000100483 GTEx
HGNC ID HGNC:20352 ENTREZGENE
Human Proteome Map VCPKMT Human Proteome Map
InterPro Methyltransf_16 UniProtKB/Swiss-Prot
  SAM-dependent_MTases UniProtKB/Swiss-Prot
KEGG Report hsa:79609 UniProtKB/Swiss-Prot
NCBI Gene 79609 ENTREZGENE
OMIM 615260 OMIM
PANTHER PROTEIN-LYSINE METHYLTRANSFERASE METTL21D UniProtKB/Swiss-Prot
  PTHR14614 UniProtKB/Swiss-Prot
Pfam Methyltransf_16 UniProtKB/Swiss-Prot
PharmGKB PA134866014 PharmGKB
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot
UniProt B7ZLA3 ENTREZGENE
  B7ZLA4 ENTREZGENE
  MT21D_HUMAN UniProtKB/Swiss-Prot
  Q2M2X3 ENTREZGENE
  Q86T12 ENTREZGENE
  Q9H867 ENTREZGENE
UniProt Secondary B7ZLA3 UniProtKB/Swiss-Prot
  B7ZLA4 UniProtKB/Swiss-Prot
  Q2M2X3 UniProtKB/Swiss-Prot
  Q86T12 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-12 VCPKMT  valosin containing protein lysine methyltransferase    valosin containing protein lysine (K) methyltransferase  Symbol and/or name change 5135510 APPROVED
2013-10-22 VCPKMT  valosin containing protein lysine (K) methyltransferase  METTL21D  methyltransferase like 21D  Symbol and/or name change 5135510 APPROVED
2011-07-27 METTL21D  methyltransferase like 21D  C14orf138  chromosome 14 open reading frame 138  Symbol and/or name change 5135510 APPROVED