VGLL3 (vestigial like family member 3) - Rat Genome Database

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Gene: VGLL3 (vestigial like family member 3) Homo sapiens
Analyze
Symbol: VGLL3
Name: vestigial like family member 3
RGD ID: 1602804
HGNC Page HGNC:24327
Description: Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: colon carcinoma related protein; DKFZp686O1845; FLJ38507; transcription cofactor vestigial-like protein 3; vestigial like 3; vestigial-like 3; vestigial-like family member 3; VGL-3; VGL3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38386,937,973 - 86,991,149 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl386,876,388 - 86,991,149 (-)EnsemblGRCh38hg38GRCh38
GRCh37386,987,123 - 87,040,299 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36387,069,813 - 87,122,947 (-)NCBINCBI36Build 36hg18NCBI36
Celera387,739,047 - 87,793,404 (-)NCBICelera
Cytogenetic Map3p12.1NCBI
HuRef387,000,438 - 87,053,543 (-)NCBIHuRef
CHM1_1386,939,749 - 86,992,814 (-)NCBICHM1_1
T2T-CHM13v2.0387,012,305 - 87,065,510 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-hydroxypropanoic acid  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
8-Br-cAMP  (EXP)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP)
benzo[a]pyrene  (EXP)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
butanal  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
chloroprene  (ISO)
cisplatin  (EXP)
cyclosporin A  (EXP)
dexamethasone  (EXP)
dibutyl phthalate  (ISO)
dimethylarsinous acid  (EXP)
dioxygen  (ISO)
dorsomorphin  (EXP)
enniatin  (EXP)
entinostat  (EXP)
epoxiconazole  (ISO)
fenamidone  (ISO)
folic acid  (EXP,ISO)
fulvestrant  (EXP)
genistein  (ISO)
indometacin  (EXP)
isoprenaline  (ISO)
ketoconazole  (EXP)
lead diacetate  (ISO)
lead(0)  (EXP)
lipopolysaccharide  (EXP)
mercury dibromide  (EXP)
methoxychlor  (ISO)
methylmercury chloride  (EXP)
nitrofen  (ISO)
panobinostat  (EXP)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenylmercury acetate  (EXP)
rac-lactic acid  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (EXP)
SB 431542  (EXP)
silicon dioxide  (EXP)
sodium arsenite  (EXP,ISO)
sulforaphane  (EXP)
temozolomide  (EXP)
tetrachloromethane  (ISO)
thiram  (EXP)
titanium dioxide  (ISO)
trichostatin A  (EXP)
valproic acid  (EXP)
vorinostat  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA,IEA)

Molecular Function

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:11819507   PMID:12376544   PMID:12477932   PMID:14702039   PMID:15146197   PMID:16344560   PMID:19336002   PMID:20842732   PMID:21102462   PMID:21873635   PMID:22219177   PMID:23152581  
PMID:23251661   PMID:23415753   PMID:23449627   PMID:26618866   PMID:26972000   PMID:27992404   PMID:29180619   PMID:31138678   PMID:31992826   PMID:32296183   PMID:32385107   PMID:32803756  
PMID:33060790   PMID:33649458   PMID:34679187   PMID:35198878   PMID:35256555   PMID:35434822   PMID:35559673   PMID:35766997   PMID:35941675   PMID:36754961   PMID:38348744  


Genomics

Comparative Map Data
VGLL3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38386,937,973 - 86,991,149 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl386,876,388 - 86,991,149 (-)EnsemblGRCh38hg38GRCh38
GRCh37386,987,123 - 87,040,299 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36387,069,813 - 87,122,947 (-)NCBINCBI36Build 36hg18NCBI36
Celera387,739,047 - 87,793,404 (-)NCBICelera
Cytogenetic Map3p12.1NCBI
HuRef387,000,438 - 87,053,543 (-)NCBIHuRef
CHM1_1386,939,749 - 86,992,814 (-)NCBICHM1_1
T2T-CHM13v2.0387,012,305 - 87,065,510 (-)NCBIT2T-CHM13v2.0
Vgll3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391665,612,075 - 65,663,254 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1665,612,143 - 65,663,254 (+)EnsemblGRCm39 Ensembl
GRCm381665,815,189 - 65,866,368 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1665,815,257 - 65,866,368 (+)EnsemblGRCm38mm10GRCm38
MGSCv371665,815,878 - 65,863,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361665,733,678 - 65,781,326 (+)NCBIMGSCv36mm8
MGSCv361666,265,561 - 66,314,128 (+)NCBIMGSCv36mm8
Celera1666,081,364 - 66,128,723 (+)NCBICelera
Cytogenetic Map16C1.3NCBI
cM Map1637.34NCBI
Vgll3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81117,089,484 - 17,136,501 (+)NCBIGRCr8
mRatBN7.2113,642,993 - 3,692,590 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl113,643,069 - 3,689,140 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0113,119,509 - 3,168,883 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl113,119,885 - 3,164,751 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0113,097,556 - 3,146,588 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4113,348,763 - 3,394,087 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera113,617,060 - 3,666,333 (+)NCBICelera
Cytogenetic Map11p12NCBI
Vgll3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554076,258,251 - 6,287,397 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554076,247,557 - 6,293,133 (+)NCBIChiLan1.0ChiLan1.0
VGLL3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2287,005,764 - 87,133,600 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1387,087,730 - 87,138,166 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0387,066,497 - 87,119,625 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1389,183,186 - 89,233,290 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl389,165,559 - 89,233,239 (-)Ensemblpanpan1.1panPan2
VGLL3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1311,037,001 - 1,151,812 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl311,036,652 - 1,143,670 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha311,078,747 - 1,196,263 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0311,020,681 - 1,138,576 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl311,020,693 - 1,066,261 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.131999,127 - 1,046,551 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0311,047,879 - 1,095,314 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0311,350,874 - 1,468,572 (+)NCBIUU_Cfam_GSD_1.0
Vgll3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049712,528,231 - 2,583,681 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366102,528,670 - 2,577,951 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366102,528,420 - 2,579,156 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VGLL3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13168,790,207 - 168,836,927 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113168,790,024 - 168,839,962 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213179,675,642 - 179,725,107 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VGLL3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12289,927,526 - 89,972,790 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2289,928,227 - 89,973,245 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604176,754,073 - 76,804,505 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vgll3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247893,232,287 - 3,271,600 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247893,226,581 - 3,271,940 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VGLL3
32 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p12.2-11.2(chr3:80320584-87468216)x3 copy number gain See cases [RCV000051499] Chr3:80320584..87468216 [GRCh38]
Chr3:80369734..87517366 [GRCh37]
Chr3:80452424..87600056 [NCBI36]
Chr3:3p12.2-11.2
uncertain significance
GRCh38/hg38 3p12.2-11.1(chr3:82912987-90179222)x1 copy number loss See cases [RCV000051542] Chr3:82912987..90179222 [GRCh38]
Chr3:82962138..90228372 [GRCh37]
Chr3:83044828..90311062 [NCBI36]
Chr3:3p12.2-11.1
pathogenic
GRCh38/hg38 3p12.2-11.1(chr3:83366150-88146360)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053959]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053959]|See cases [RCV000053959] Chr3:83366150..88146360 [GRCh38]
Chr3:83415301..88195510 [GRCh37]
Chr3:83497991..88278200 [NCBI36]
Chr3:3p12.2-11.1
uncertain significance
NM_016206.2(VGLL3):c.355G>A (p.Glu119Lys) single nucleotide variant Malignant melanoma [RCV000066198] Chr3:86978574 [GRCh38]
Chr3:87027724 [GRCh37]
Chr3:87110414 [NCBI36]
Chr3:3p12.1
not provided
NM_016206.2(VGLL3):c.287G>A (p.Gly96Glu) single nucleotide variant Malignant melanoma [RCV000066199] Chr3:86978642 [GRCh38]
Chr3:87027792 [GRCh37]
Chr3:87110482 [NCBI36]
Chr3:3p12.1
not provided
NM_016206.2(VGLL3):c.937+6219G>A single nucleotide variant Lung cancer [RCV000093787] Chr3:86962371 [GRCh38]
Chr3:87011521 [GRCh37]
Chr3:3p12.1
uncertain significance
GRCh38/hg38 3p12.3-11.1(chr3:76764260-89682935)x1 copy number loss See cases [RCV000135700] Chr3:76764260..89682935 [GRCh38]
Chr3:76813411..89732085 [GRCh37]
Chr3:76896101..89814775 [NCBI36]
Chr3:3p12.3-11.1
likely pathogenic
GRCh38/hg38 3p12.1-11.2(chr3:86917979-87234450)x1 copy number loss See cases [RCV000136698] Chr3:86917979..87234450 [GRCh38]
Chr3:86967129..87283600 [GRCh37]
Chr3:87049819..87366290 [NCBI36]
Chr3:3p12.1-11.2
uncertain significance
GRCh38/hg38 3p14.3-11.1(chr3:57140424-90259960)x1 copy number loss See cases [RCV000139626] Chr3:57140424..90259960 [GRCh38]
Chr3:57174452..90309110 [GRCh37]
Chr3:57149492..90391800 [NCBI36]
Chr3:3p14.3-11.1
pathogenic
GRCh38/hg38 3p13-11.1(chr3:73824871-90453699)x1 copy number loss See cases [RCV000141881] Chr3:73824871..90453699 [GRCh38]
Chr3:73874022..90502849 [GRCh37]
Chr3:73956712..90585539 [NCBI36]
Chr3:3p13-11.1
pathogenic
GRCh38/hg38 3p12.3-11.1(chr3:74649382-89495681)x1 copy number loss See cases [RCV000143665] Chr3:74649382..89495681 [GRCh38]
Chr3:74698533..89544831 [GRCh37]
Chr3:74781223..89627521 [NCBI36]
Chr3:3p12.3-11.1
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29
pathogenic
NM_016206.4(VGLL3):c.877G>A (p.Ala293Thr) single nucleotide variant not specified [RCV004296269] Chr3:86968650 [GRCh38]
Chr3:87017800 [GRCh37]
Chr3:3p12.1
uncertain significance
GRCh37/hg19 3p12.1-11.2(chr3:86841600-87862816)x3 copy number gain not provided [RCV001005452] Chr3:86841600..87862816 [GRCh37]
Chr3:3p12.1-11.2
uncertain significance
GRCh37/hg19 3p13-q12.1(chr3:72488757-99614758)x3 copy number gain not provided [RCV002221455] Chr3:72488757..99614758 [GRCh37]
Chr3:3p13-q12.1
likely pathogenic
GRCh37/hg19 3p12.1-11.2(chr3:86841601-87862816)x3 copy number gain not provided [RCV002473443] Chr3:86841601..87862816 [GRCh37]
Chr3:3p12.1-11.2
uncertain significance
NM_016206.4(VGLL3):c.238G>A (p.Glu80Lys) single nucleotide variant not specified [RCV004086212] Chr3:86978691 [GRCh38]
Chr3:87027841 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.817C>T (p.Pro273Ser) single nucleotide variant not specified [RCV004190570] Chr3:86968710 [GRCh38]
Chr3:87017860 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.593C>T (p.Ala198Val) single nucleotide variant not specified [RCV004122778] Chr3:86968934 [GRCh38]
Chr3:87018084 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.622C>A (p.Pro208Thr) single nucleotide variant not specified [RCV004096036] Chr3:86968905 [GRCh38]
Chr3:87018055 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.29C>T (p.Pro10Leu) single nucleotide variant not specified [RCV004226428] Chr3:86990715 [GRCh38]
Chr3:87039865 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.381G>T (p.Met127Ile) single nucleotide variant not specified [RCV004148987] Chr3:86978548 [GRCh38]
Chr3:87027698 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.781C>T (p.Pro261Ser) single nucleotide variant not specified [RCV004101371] Chr3:86968746 [GRCh38]
Chr3:87017896 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.470C>A (p.Pro157His) single nucleotide variant not specified [RCV004241014] Chr3:86969057 [GRCh38]
Chr3:87018207 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.103C>A (p.Pro35Thr) single nucleotide variant not specified [RCV004201867] Chr3:86990641 [GRCh38]
Chr3:87039791 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.715C>T (p.Arg239Cys) single nucleotide variant not specified [RCV004081603] Chr3:86968812 [GRCh38]
Chr3:87017962 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.751G>T (p.Ala251Ser) single nucleotide variant not specified [RCV004272224] Chr3:86968776 [GRCh38]
Chr3:87017926 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.407G>A (p.Ser136Asn) single nucleotide variant not specified [RCV004273745] Chr3:86969120 [GRCh38]
Chr3:87018270 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.53A>G (p.Tyr18Cys) single nucleotide variant not specified [RCV004360565] Chr3:86990691 [GRCh38]
Chr3:87039841 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.670G>A (p.Asp224Asn) single nucleotide variant not specified [RCV004354916] Chr3:86968857 [GRCh38]
Chr3:87018007 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.225A>G (p.Lys75=) single nucleotide variant not provided [RCV003437918] Chr3:86978704 [GRCh38]
Chr3:87027854 [GRCh37]
Chr3:3p12.1
likely benign
NM_016206.4(VGLL3):c.105G>A (p.Pro35=) single nucleotide variant not provided [RCV003437919] Chr3:86990639 [GRCh38]
Chr3:87039789 [GRCh37]
Chr3:3p12.1
likely benign
NM_016206.4(VGLL3):c.102G>C (p.Gln34His) single nucleotide variant not specified [RCV004480418] Chr3:86990642 [GRCh38]
Chr3:87039792 [GRCh37]
Chr3:3p12.1
likely benign
NM_016206.4(VGLL3):c.227A>C (p.Asp76Ala) single nucleotide variant not specified [RCV004480419] Chr3:86978702 [GRCh38]
Chr3:87027852 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.229C>A (p.Gln77Lys) single nucleotide variant not specified [RCV004480420] Chr3:86978700 [GRCh38]
Chr3:87027850 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.643G>A (p.Val215Met) single nucleotide variant not specified [RCV004482405] Chr3:86968884 [GRCh38]
Chr3:87018034 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.887G>T (p.Gly296Val) single nucleotide variant not specified [RCV004482407] Chr3:86968640 [GRCh38]
Chr3:87017790 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.890C>G (p.Ala297Gly) single nucleotide variant not specified [RCV004482408] Chr3:86968637 [GRCh38]
Chr3:87017787 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.427C>T (p.Arg143Trp) single nucleotide variant not specified [RCV004480421] Chr3:86969100 [GRCh38]
Chr3:87018250 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.757T>A (p.Ser253Thr) single nucleotide variant not specified [RCV004482406] Chr3:86968770 [GRCh38]
Chr3:87017920 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.428G>A (p.Arg143Gln) single nucleotide variant not specified [RCV004681012] Chr3:86969099 [GRCh38]
Chr3:87018249 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.470C>T (p.Pro157Leu) single nucleotide variant not specified [RCV004681013] Chr3:86969057 [GRCh38]
Chr3:87018207 [GRCh37]
Chr3:3p12.1
uncertain significance
NM_016206.4(VGLL3):c.364A>T (p.Ile122Phe) single nucleotide variant not specified [RCV004681015] Chr3:86978565 [GRCh38]
Chr3:87027715 [GRCh37]
Chr3:3p12.1
uncertain significance
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR24-2hsa-miR-24-3pMirtarbaseexternal_infoSequencingFunctional MTI (Weak)20138800
MIR24-1hsa-miR-24-3pMirtarbaseexternal_infoSequencingFunctional MTI (Weak)20138800

Predicted Target Of
Summary Value
Count of predictions:3937
Count of miRNA genes:1276
Interacting mature miRNAs:1659
Transcripts:ENST00000383698, ENST00000398399, ENST00000494229
Prediction methods: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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
597272443GWAS1368517_Hhigh density lipoprotein cholesterol measurement QTL GWAS1368517 (human)2e-08high density lipoprotein cholesterol measurementblood triglyceride level (CMO:0000118)38698839386988394Human
597215227GWAS1311301_Hbody height QTL GWAS1311301 (human)9e-10body height (VT:0001253)body height (CMO:0000106)38694307286943073Human
597350943GWAS1447017_Hbody height QTL GWAS1447017 (human)2e-66body height (VT:0001253)body height (CMO:0000106)38698285486982855Human
597135231GWAS1231305_Hbody height QTL GWAS1231305 (human)5e-11body height (VT:0001253)body height (CMO:0000106)38698285486982855Human
597147804GWAS1243878_Hprostate carcinoma QTL GWAS1243878 (human)7e-08prostate carcinoma38694244886942450Human
596958200GWAS1077719_Hhigh density lipoprotein cholesterol measurement QTL GWAS1077719 (human)1e-09high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)38698839386988394Human
597151194GWAS1247268_Hprostate carcinoma QTL GWAS1247268 (human)5e-18prostate carcinoma38694244886942450Human
597322295GWAS1418369_Htriglyceride measurement QTL GWAS1418369 (human)1e-11triglyceride measurementblood triglyceride level (CMO:0000118)38698839386988394Human
597036057GWAS1132131_Hhigh density lipoprotein cholesterol measurement QTL GWAS1132131 (human)3e-11high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)38698839386988394Human
597267126GWAS1363200_Htriglyceride measurement QTL GWAS1363200 (human)6e-09triglyceride measurementblood triglyceride level (CMO:0000118)38698839386988394Human
597257098GWAS1353172_Htriglyceride measurement QTL GWAS1353172 (human)4e-09triglyceride measurementblood triglyceride level (CMO:0000118)38698839386988394Human
597023694GWAS1119768_Hbreast carcinoma QTL GWAS1119768 (human)1e-09mammary gland integrity trait (VT:0010552)blood high density lipoprotein cholesterol level (CMO:0000052)38698839386988394Human
597145483GWAS1241557_Hprostate carcinoma QTL GWAS1241557 (human)2e-23prostate carcinoma38694244886942450Human
597273287GWAS1369361_Htriglyceride measurement QTL GWAS1369361 (human)5e-09triglyceride measurementblood triglyceride level (CMO:0000118)38698839386988394Human
597035465GWAS1131539_Htriglyceride measurement QTL GWAS1131539 (human)1e-10triglyceride measurementblood triglyceride level (CMO:0000118)38698839386988394Human

Markers in Region
A004P25  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,987,252 - 86,987,352UniSTSGRCh37
Build 36387,069,942 - 87,070,042RGDNCBI36
Celera387,739,176 - 87,739,276RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,000,567 - 87,000,667UniSTS
GeneMap99-GB4 RH Map3262.81UniSTS
NCBI RH Map3683.7UniSTS
SHGC-68425  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,990,443 - 86,990,532UniSTSGRCh37
Build 36387,073,133 - 87,073,222RGDNCBI36
Celera387,742,367 - 87,742,456RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,003,758 - 87,003,847UniSTS
TNG Radiation Hybrid Map352661.0UniSTS
RH102693  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,996,060 - 86,996,188UniSTSGRCh37
Build 36387,078,750 - 87,078,878RGDNCBI36
Celera387,747,986 - 87,748,114RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,009,375 - 87,009,503UniSTS
GeneMap99-GB4 RH Map3261.42UniSTS
G20437  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,989,852 - 86,990,035UniSTSGRCh37
Build 36387,072,542 - 87,072,725RGDNCBI36
Celera387,741,776 - 87,741,959RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,003,167 - 87,003,350UniSTS
A005R17  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,989,852 - 86,990,035UniSTSGRCh37
Build 36387,072,542 - 87,072,725RGDNCBI36
Celera387,741,776 - 87,741,959RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,003,167 - 87,003,350UniSTS
GeneMap99-GB4 RH Map3264.48UniSTS
NCBI RH Map3683.7UniSTS
SHGC-77133  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,991,571 - 86,991,848UniSTSGRCh37
Build 36387,074,261 - 87,074,538RGDNCBI36
Celera387,743,495 - 87,743,773RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,004,886 - 87,005,164UniSTS
TNG Radiation Hybrid Map352616.0UniSTS
GeneMap99-GB4 RH Map3264.48UniSTS
NCBI RH Map3683.7UniSTS
D15S1269  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,987,157 - 86,987,298UniSTSGRCh37
Build 36387,069,847 - 87,069,988RGDNCBI36
Celera387,739,081 - 87,739,222RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,000,472 - 87,000,613UniSTS
SHGC-77128  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37387,037,603 - 87,037,773UniSTSGRCh37
Build 36387,120,293 - 87,120,463RGDNCBI36
Celera387,789,520 - 87,789,690RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,050,913 - 87,051,083UniSTS
TNG Radiation Hybrid Map352590.0UniSTS
GeneMap99-GB4 RH Map3261.8UniSTS
NCBI RH Map3679.4UniSTS
G20685  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,990,487 - 86,990,592UniSTSGRCh37
Build 36387,073,177 - 87,073,282RGDNCBI36
Celera387,742,411 - 87,742,516RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,003,802 - 87,003,907UniSTS
A006B39  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,990,487 - 86,990,592UniSTSGRCh37
Build 36387,073,177 - 87,073,282RGDNCBI36
Celera387,742,411 - 87,742,516RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,003,802 - 87,003,907UniSTS
GeneMap99-GB4 RH Map3264.48UniSTS
NCBI RH Map3683.7UniSTS
RH45063  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,992,713 - 86,992,836UniSTSGRCh37
Build 36387,075,403 - 87,075,526RGDNCBI36
Celera387,744,638 - 87,744,761RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,006,027 - 87,006,150UniSTS
GeneMap99-GB4 RH Map3262.81UniSTS
NCBI RH Map3683.7UniSTS
RH69879  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,990,642 - 86,990,762UniSTSGRCh37
Build 36387,073,332 - 87,073,452RGDNCBI36
Celera387,742,566 - 87,742,686RGD
Cytogenetic Map3p12.1UniSTS
HuRef387,003,957 - 87,004,077UniSTS
GeneMap99-GB4 RH Map3264.48UniSTS
NCBI RH Map3683.7UniSTS
UniSTS:487342  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37386,987,204 - 86,988,568UniSTSGRCh37
Celera387,739,128 - 87,740,492UniSTS
HuRef387,000,519 - 87,001,883UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2379 2788 2232 4925 1699 2274 6 602 1263 444 2249 6531 5801 45 3698 1 801 1719 1563 174 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001320493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001320494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_016206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006713138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054346475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA455617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC108709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF099505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI379920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK095826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC017383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC062478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC094780 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX369995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX391744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF995043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CN287582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR936700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA828655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB319377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HH756203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HH756215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HH792471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HH792483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENST00000383698   ⟹   ENSP00000373199
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl386,961,906 - 86,991,119 (-)Ensembl
Ensembl Acc Id: ENST00000398399   ⟹   ENSP00000381436
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl386,937,973 - 86,991,149 (-)Ensembl
Ensembl Acc Id: ENST00000494229   ⟹   ENSP00000419115
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl386,968,703 - 86,990,702 (-)Ensembl
Ensembl Acc Id: ENST00000637106   ⟹   ENSP00000489678
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl386,876,388 - 86,968,631 (-)Ensembl
RefSeq Acc Id: NM_001320493   ⟹   NP_001307422
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38386,961,906 - 86,991,149 (-)NCBI
CHM1_1386,963,667 - 86,992,830 (-)NCBI
T2T-CHM13v2.0387,036,241 - 87,065,510 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001320494   ⟹   NP_001307423
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38386,937,973 - 86,991,149 (-)NCBI
CHM1_1386,939,745 - 86,992,830 (-)NCBI
T2T-CHM13v2.0387,012,305 - 87,065,510 (-)NCBI
Sequence:
RefSeq Acc Id: NM_016206   ⟹   NP_057290
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38386,937,973 - 86,991,149 (-)NCBI
GRCh37386,987,123 - 87,040,412 (-)NCBI
Build 36387,069,813 - 87,122,947 (-)NCBI Archive
Celera387,739,047 - 87,793,404 (-)RGD
HuRef387,000,438 - 87,053,543 (-)RGD
CHM1_1386,939,745 - 86,992,830 (-)NCBI
T2T-CHM13v2.0387,012,305 - 87,065,510 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006713138   ⟹   XP_006713201
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38386,937,973 - 86,991,149 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054346475   ⟹   XP_054202450
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0387,012,305 - 87,065,510 (-)NCBI
RefSeq Acc Id: NP_057290   ⟸   NM_016206
- Peptide Label: isoform 1
- UniProtKB: A8MV65 (UniProtKB/Swiss-Prot),   D3DU37 (UniProtKB/Swiss-Prot),   Q504T7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006713201   ⟸   XM_006713138
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001307423   ⟸   NM_001320494
- Peptide Label: isoform 3
- Sequence:
RefSeq Acc Id: NP_001307422   ⟸   NM_001320493
- Peptide Label: isoform 2
- UniProtKB: A8MV65 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSP00000381436   ⟸   ENST00000398399
Ensembl Acc Id: ENSP00000489678   ⟸   ENST00000637106
Ensembl Acc Id: ENSP00000419115   ⟸   ENST00000494229
Ensembl Acc Id: ENSP00000373199   ⟸   ENST00000383698
RefSeq Acc Id: XP_054202450   ⟸   XM_054346475
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A8MV65-F1-model_v2 AlphaFold A8MV65 1-326 view protein structure

Promoters
RGD ID:6865026
Promoter ID:EPDNEW_H5678
Type:initiation region
Name:VGLL3_2
Description:vestigial like family member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H5679  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38386,990,860 - 86,990,920EPDNEW
RGD ID:6865028
Promoter ID:EPDNEW_H5679
Type:initiation region
Name:VGLL3_1
Description:vestigial like family member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H5678  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38386,991,121 - 86,991,181EPDNEW
RGD ID:6800985
Promoter ID:HG_KWN:45593
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3
Transcripts:ENST00000383698,   NM_016206
Position:
Human AssemblyChrPosition (strand)Source
Build 36387,122,546 - 87,123,046 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:24327 AgrOrtholog
COSMIC VGLL3 COSMIC
Ensembl Genes ENSG00000206538 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000383698 ENTREZGENE
  ENST00000383698.3 UniProtKB/Swiss-Prot
  ENST00000398399 ENTREZGENE
  ENST00000398399.7 UniProtKB/Swiss-Prot
  ENST00000494229.1 UniProtKB/TrEMBL
  ENST00000637106.1 UniProtKB/TrEMBL
GTEx ENSG00000206538 GTEx
HGNC ID HGNC:24327 ENTREZGENE
Human Proteome Map VGLL3 Human Proteome Map
InterPro TDU_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vg_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:389136 UniProtKB/Swiss-Prot
NCBI Gene 389136 ENTREZGENE
OMIM 609980 OMIM
PANTHER PTHR15950 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSCRIPTION COFACTOR VESTIGIAL-LIKE PROTEIN 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Vg_Tdu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142670628 PharmGKB
SMART TDU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1B0GTF5_HUMAN UniProtKB/TrEMBL
  A8MV65 ENTREZGENE
  D3DU37 ENTREZGENE
  H7C571_HUMAN UniProtKB/TrEMBL
  Q504T7 ENTREZGENE
  VGLL3_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary D3DU37 UniProtKB/Swiss-Prot
  Q504T7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-01 VGLL3  vestigial like family member 3    vestigial-like family member 3  Symbol and/or name change 5135510 APPROVED
2014-03-05 VGLL3  vestigial-like family member 3    vestigial like 3 (Drosophila)  Symbol and/or name change 5135510 APPROVED