VNN1 (vanin 1) - Rat Genome Database

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Gene: VNN1 (vanin 1) Homo sapiens
Analyze
Symbol: VNN1
Name: vanin 1
RGD ID: 1320770
HGNC Page HGNC:12705
Description: Enables pantetheine hydrolase activity. Involved in pantothenate metabolic process. Predicted to be located in azurophil granule membrane; extracellular region; and plasma membrane. Biomarker of pancreatic ductal adenocarcinoma.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: HDLCQ8; MGC116930; MGC116931; MGC116932; MGC116933; pantetheinase; pantetheine hydrolase; Tiff66; vanin-1; vannin 1; vascular non-inflammatory molecule 1
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
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
GRCh386132,680,849 - 132,714,055 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6132,680,849 - 132,714,055 (-)EnsemblGRCh38hg38GRCh38
GRCh376133,001,988 - 133,035,194 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366133,044,422 - 133,076,881 (-)NCBINCBI36Build 36hg18NCBI36
Build 346133,044,422 - 133,076,881NCBI
Celera6133,748,822 - 133,782,014 (-)NCBICelera
Cytogenetic Map6q23.2NCBI
HuRef6130,576,916 - 130,610,106 (-)NCBIHuRef
CHM1_16133,265,672 - 133,298,869 (-)NCBICHM1_1
T2T-CHM13v2.06133,875,818 - 133,909,022 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,4-dinitrotoluene  (ISO)
2,6-dinitrotoluene  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-chloropropane-1,2-diol  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
6-propyl-2-thiouracil  (ISO)
acetamide  (ISO)
aldehydo-D-glucosamine  (ISO)
allyl alcohol  (EXP)
alpha-Zearalanol  (ISO)
amiodarone  (ISO)
amphotericin B  (EXP)
arsenous acid  (EXP)
azathioprine  (EXP)
benzbromarone  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-D-glucosamine  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (ISO)
bisphenol F  (ISO)
bosentan  (EXP)
buspirone  (ISO)
butanal  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroform  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
ciglitazone  (EXP)
cisplatin  (EXP)
Citreoviridin  (EXP,ISO)
clofibrate  (ISO)
Clofop  (EXP)
cobalt dichloride  (ISO)
copper(II) sulfate  (EXP)
corn oil  (ISO)
cyanocob(III)alamin  (ISO)
cyclosporin A  (EXP,ISO)
cysteamine  (ISO)
dapagliflozin  (ISO)
decabromodiphenyl ether  (ISO)
diarsenic trioxide  (EXP)
dibenzofurans  (ISO)
Dibutyl phosphate  (EXP)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dicrotophos  (EXP)
diethylstilbestrol  (ISO)
dimethylarsinic acid  (ISO)
diquat  (ISO)
diuron  (ISO)
endosulfan  (ISO)
epoxiconazole  (ISO)
ethylene glycol  (EXP,ISO)
fenofibrate  (EXP,ISO)
finasteride  (ISO)
fipronil  (ISO)
flutamide  (ISO)
folic acid  (ISO)
formaldehyde  (EXP)
fructose  (ISO)
gemfibrozil  (ISO)
gentamycin  (ISO)
glafenine  (ISO)
glutathione  (ISO)
glycine betaine  (ISO)
GW 4064  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (ISO)
inulin  (ISO)
L-ethionine  (ISO)
L-methionine  (ISO)
leflunomide  (EXP,ISO)
metformin  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methylarsonic acid  (ISO)
Muraglitazar  (ISO)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (ISO)
nefazodone  (ISO)
nimesulide  (ISO)
nitrofen  (ISO)
ochratoxin A  (ISO)
oleic acid  (EXP)
omeprazole  (ISO)
orphenadrine  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorononanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (ISO)
phenformin  (ISO)
phenobarbital  (ISO)
phenol  (EXP)
piperonyl butoxide  (ISO)
pirinixic acid  (ISO)
pravastatin  (ISO)
progesterone  (EXP)
propanal  (EXP)
quercetin  (EXP)
reactive oxygen species  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
spirotetramat  (ISO)
streptozocin  (ISO)
Tesaglitazar  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
trichloroethene  (ISO)
triphenyl phosphate  (EXP)
tris(2-butoxyethyl) phosphate  (EXP)
troglitazone  (EXP,ISO)
valdecoxib  (ISO)
valproic acid  (ISO)
zaragozic acid A  (ISO)
zinc atom  (EXP,ISO)
zinc(0)  (EXP,ISO)
zoledronic acid  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. PSMD11, PTPRM and PTPRB as novel biomarkers of pancreatic cancer progression. Sahni S, etal., Biochim Biophys Acta Gen Subj. 2020 Nov;1864(11):129682. doi: 10.1016/j.bbagen.2020.129682. Epub 2020 Jul 12.
Additional References at PubMed
PMID:8934567   PMID:9790769   PMID:10567687   PMID:11491533   PMID:12477932   PMID:14574404   PMID:14702039   PMID:14966568   PMID:15084671   PMID:15282320   PMID:15489334   PMID:16335952  
PMID:17145956   PMID:17312006   PMID:18043751   PMID:19322213   PMID:19490893   PMID:20571492   PMID:20641033   PMID:21325602   PMID:21544065   PMID:21550219   PMID:21873635   PMID:21907259  
PMID:23185446   PMID:23376485   PMID:23534352   PMID:23949622   PMID:23978960   PMID:24106341   PMID:24140347   PMID:24687856   PMID:24702142   PMID:24751833   PMID:25233454   PMID:25478849  
PMID:25910714   PMID:26343328   PMID:27317936   PMID:28316092   PMID:28576495   PMID:30791405   PMID:31404995   PMID:33656956   PMID:33660365   PMID:33754072   PMID:33961781   PMID:34275284  
PMID:38607943  


Genomics

Comparative Map Data
VNN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386132,680,849 - 132,714,055 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6132,680,849 - 132,714,055 (-)EnsemblGRCh38hg38GRCh38
GRCh376133,001,988 - 133,035,194 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366133,044,422 - 133,076,881 (-)NCBINCBI36Build 36hg18NCBI36
Build 346133,044,422 - 133,076,881NCBI
Celera6133,748,822 - 133,782,014 (-)NCBICelera
Cytogenetic Map6q23.2NCBI
HuRef6130,576,916 - 130,610,106 (-)NCBIHuRef
CHM1_16133,265,672 - 133,298,869 (-)NCBICHM1_1
T2T-CHM13v2.06133,875,818 - 133,909,022 (-)NCBIT2T-CHM13v2.0
Vnn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391023,770,586 - 23,781,242 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1023,770,586 - 23,781,241 (+)EnsemblGRCm39 Ensembl
GRCm381023,894,688 - 23,905,344 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1023,894,688 - 23,905,343 (+)EnsemblGRCm38mm10GRCm38
MGSCv371023,614,494 - 23,625,149 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361023,573,041 - 23,594,755 (+)NCBIMGSCv36mm8
Celera1024,828,202 - 24,838,840 (+)NCBICelera
Cytogenetic Map10A4NCBI
cM Map1011.33NCBI
Vnn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8123,356,324 - 23,366,629 (-)NCBIGRCr8
mRatBN7.2121,537,084 - 21,547,395 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,537,094 - 21,547,395 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx121,316,351 - 21,326,676 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0127,316,396 - 27,326,721 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0121,513,723 - 21,524,007 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,614,832 - 22,625,134 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,614,783 - 22,625,204 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,089,365 - 24,099,667 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,087,290 - 22,097,592 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1122,090,508 - 22,100,537 (-)NCBI
Celera120,280,201 - 20,290,503 (-)NCBICelera
Cytogenetic Map1p12NCBI
Vnn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543613,238,603 - 13,259,577 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543613,238,307 - 13,266,800 (-)NCBIChiLan1.0ChiLan1.0
VNN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25152,665,525 - 152,697,484 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16150,572,617 - 150,604,502 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06130,459,268 - 130,491,167 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16134,566,110 - 134,598,784 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6134,566,117 - 134,598,784 (-)Ensemblpanpan1.1panPan2
VNN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1125,678,039 - 25,704,579 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl125,678,042 - 25,696,807 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha126,742,992 - 26,770,993 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0125,767,887 - 25,802,756 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl125,767,890 - 25,796,358 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1125,690,559 - 25,711,049 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0125,596,017 - 25,624,588 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0125,852,617 - 25,901,434 (-)NCBIUU_Cfam_GSD_1.0
Vnn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946120,920,545 - 120,951,976 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936560701,892 - 729,526 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936560701,857 - 729,516 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VNN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl131,000,255 - 31,024,505 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1131,003,338 - 31,023,731 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2134,520,052 - 34,544,689 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Vnn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247536,867,953 - 6,892,186 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247536,869,269 - 6,892,217 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VNN1
45 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NC_000006.12:g.132714186A>C single nucleotide variant RECLASSIFIED - VNN1 POLYMORPHISM [RCV000006608] Chr6:132714186 [GRCh38]
Chr6:133035325 [GRCh37]
Chr6:6q23.2		 association|benign
NM_004666.2(VNN1):c.341+2900C>A single nucleotide variant Lung cancer [RCV000096535] Chr6:132708809 [GRCh38]
Chr6:133029948 [GRCh37]
Chr6:6q23.2		 uncertain significance
GRCh38/hg38 6q23.2(chr6:132455272-133141153)x3 copy number gain See cases [RCV000053388] Chr6:132455272..133141153 [GRCh38]
Chr6:132776411..133462292 [GRCh37]
Chr6:132818104..133503985 [NCBI36]
Chr6:6q23.2		 uncertain significance
NM_004666.2(VNN1):c.1143G>A (p.Gly381=) single nucleotide variant Malignant melanoma [RCV000067126] Chr6:132692268 [GRCh38]
Chr6:133013407 [GRCh37]
Chr6:133055100 [NCBI36]
Chr6:6q23.2		 not provided
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
NM_004666.3(VNN1):c.901C>T (p.Leu301Phe) single nucleotide variant not specified [RCV004323496] Chr6:132692510 [GRCh38]
Chr6:133013649 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.692C>T (p.Thr231Ile) single nucleotide variant not specified [RCV004329701] Chr6:132693158 [GRCh38]
Chr6:133014297 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.179T>C (p.Leu60Ser) single nucleotide variant not specified [RCV004312036] Chr6:132713857 [GRCh38]
Chr6:133034996 [GRCh37]
Chr6:6q23.2		 uncertain significance
GRCh37/hg19 6q23.2-23.3(chr6:131388023-137469640)x1 copy number loss not provided [RCV000682724] Chr6:131388023..137469640 [GRCh37]
Chr6:6q23.2-23.3		 pathogenic
GRCh37/hg19 6q23.2-23.3(chr6:132002460-137160850)x1 copy number loss not provided [RCV000682725] Chr6:132002460..137160850 [GRCh37]
Chr6:6q23.2-23.3		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6q23.2(chr6:133003344-133168463)x3 copy number gain not provided [RCV000746040] Chr6:133003344..133168463 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.1540T>C (p.Ter514Gln) single nucleotide variant not provided [RCV000956414] Chr6:132683142 [GRCh38]
Chr6:133004281 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.436G>A (p.Asp146Asn) single nucleotide variant not provided [RCV000884319] Chr6:132694088 [GRCh38]
Chr6:133015227 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.1335T>C (p.Asn445=) single nucleotide variant not provided [RCV000926725] Chr6:132684359 [GRCh38]
Chr6:133005498 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.406G>C (p.Val136Leu) single nucleotide variant not provided [RCV000961746] Chr6:132694118 [GRCh38]
Chr6:133015257 [GRCh37]
Chr6:6q23.2		 benign
GRCh37/hg19 6q23.2(chr6:132926920-133314722)x3 copy number gain not provided [RCV000849414] Chr6:132926920..133314722 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.470G>A (p.Arg157His) single nucleotide variant not provided [RCV000958583] Chr6:132694054 [GRCh38]
Chr6:133015193 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.967A>G (p.Ile323Val) single nucleotide variant not specified [RCV004301778] Chr6:132692444 [GRCh38]
Chr6:133013583 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.335G>A (p.Arg112His) single nucleotide variant not provided [RCV000888601] Chr6:132711715 [GRCh38]
Chr6:133032854 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.888G>C (p.Glu296Asp) single nucleotide variant not provided [RCV000956417] Chr6:132692523 [GRCh38]
Chr6:133013662 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.216G>A (p.Ala72=) single nucleotide variant not provided [RCV000956419] Chr6:132711834 [GRCh38]
Chr6:133032973 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.1118T>C (p.Ile373Thr) single nucleotide variant not provided [RCV000956415] Chr6:132692293 [GRCh38]
Chr6:133013432 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.974C>A (p.Ala325Glu) single nucleotide variant not provided [RCV000956416] Chr6:132692437 [GRCh38]
Chr6:133013576 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.827-3C>T single nucleotide variant not provided [RCV000956418] Chr6:132692587 [GRCh38]
Chr6:133013726 [GRCh37]
Chr6:6q23.2		 benign
NM_004666.3(VNN1):c.851C>T (p.Ser284Phe) single nucleotide variant not specified [RCV004306353] Chr6:132692560 [GRCh38]
Chr6:133013699 [GRCh37]
Chr6:6q23.2		 uncertain significance
Single allele deletion Interstitial 6q microdeletion syndrome [RCV002280353] Chr6:115941808..133892653 [GRCh38]
Chr6:6q22.1-23.2		 pathogenic
NM_004666.3(VNN1):c.334C>T (p.Arg112Cys) single nucleotide variant not provided [RCV001354159]|not specified [RCV004036700] Chr6:132711716 [GRCh38]
Chr6:133032855 [GRCh37]
Chr6:6q23.2		 uncertain significance
GRCh37/hg19 6q23.1-23.3(chr6:130769034-136009217)x1 copy number loss not provided [RCV001829086] Chr6:130769034..136009217 [GRCh37]
Chr6:6q23.1-23.3		 pathogenic
GRCh37/hg19 6q23.2(chr6:132875123-133509642)x3 copy number gain not provided [RCV001834192] Chr6:132875123..133509642 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1219A>G (p.Asn407Asp) single nucleotide variant not specified [RCV004194450] Chr6:132684475 [GRCh38]
Chr6:133005614 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.496T>C (p.Phe166Leu) single nucleotide variant not specified [RCV004156416] Chr6:132694028 [GRCh38]
Chr6:133015167 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.388A>G (p.Asn130Asp) single nucleotide variant not specified [RCV004218917] Chr6:132694136 [GRCh38]
Chr6:133015275 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.905C>T (p.Ser302Leu) single nucleotide variant not specified [RCV004127905] Chr6:132692506 [GRCh38]
Chr6:133013645 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1525T>C (p.Cys509Arg) single nucleotide variant not specified [RCV004091805] Chr6:132683157 [GRCh38]
Chr6:133004296 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.629C>T (p.Thr210Ile) single nucleotide variant not specified [RCV004111244] Chr6:132693221 [GRCh38]
Chr6:133014360 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1513G>A (p.Ala505Thr) single nucleotide variant not specified [RCV004133807] Chr6:132683169 [GRCh38]
Chr6:133004308 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.683A>G (p.His228Arg) single nucleotide variant not specified [RCV004165821] Chr6:132693167 [GRCh38]
Chr6:133014306 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.734T>C (p.Leu245Ser) single nucleotide variant not specified [RCV004208078] Chr6:132693116 [GRCh38]
Chr6:133014255 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.530A>G (p.His177Arg) single nucleotide variant not specified [RCV004163158] Chr6:132693994 [GRCh38]
Chr6:133015133 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1294G>A (p.Gly432Arg) single nucleotide variant not specified [RCV004159791] Chr6:132684400 [GRCh38]
Chr6:133005539 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.142G>A (p.Glu48Lys) single nucleotide variant not specified [RCV004126281] Chr6:132713894 [GRCh38]
Chr6:133035033 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.697G>C (p.Val233Leu) single nucleotide variant not specified [RCV004201014] Chr6:132693153 [GRCh38]
Chr6:133014292 [GRCh37]
Chr6:6q23.2		 likely benign
NM_004666.3(VNN1):c.1345C>T (p.Pro449Ser) single nucleotide variant not specified [RCV004154058] Chr6:132684349 [GRCh38]
Chr6:133005488 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.848A>T (p.Asn283Ile) single nucleotide variant not specified [RCV004120574] Chr6:132692563 [GRCh38]
Chr6:133013702 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.326G>C (p.Cys109Ser) single nucleotide variant not specified [RCV004176991] Chr6:132711724 [GRCh38]
Chr6:133032863 [GRCh37]
Chr6:6q23.2		 uncertain significance
GRCh37/hg19 6q23.2(chr6:132926527-133319409)x3 copy number gain not provided [RCV003484652] Chr6:132926527..133319409 [GRCh37]
Chr6:6q23.2		 uncertain significance
GRCh37/hg19 6q22.31-23.3(chr6:120218852-137160850)x1 copy number loss not provided [RCV003482930] Chr6:120218852..137160850 [GRCh37]
Chr6:6q22.31-23.3		 pathogenic
GRCh37/hg19 6q23.2-24.2(chr6:131569837-145572239)x3 copy number gain not specified [RCV003986663] Chr6:131569837..145572239 [GRCh37]
Chr6:6q23.2-24.2		 pathogenic
GRCh37/hg19 6q22.31-25.3(chr6:119840686-156623091)x3 copy number gain not specified [RCV003986631] Chr6:119840686..156623091 [GRCh37]
Chr6:6q22.31-25.3		 pathogenic
GRCh37/hg19 6q23.2(chr6:132951409-133081430)x3 copy number gain not specified [RCV003986641] Chr6:132951409..133081430 [GRCh37]
Chr6:6q23.2		 uncertain significance
GRCh37/hg19 6q23.2(chr6:132926526-133319409)x3 copy number gain not specified [RCV003986643] Chr6:132926526..133319409 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1393C>A (p.Pro465Thr) single nucleotide variant not specified [RCV004482611] Chr6:132683289 [GRCh38]
Chr6:133004428 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.25G>A (p.Val9Met) single nucleotide variant not specified [RCV004482612] Chr6:132714011 [GRCh38]
Chr6:133035150 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.493G>A (p.Val165Ile) single nucleotide variant not specified [RCV004482613] Chr6:132694031 [GRCh38]
Chr6:133015170 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.520G>T (p.Ala174Ser) single nucleotide variant not specified [RCV004482614] Chr6:132694004 [GRCh38]
Chr6:133015143 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.671T>A (p.Val224Glu) single nucleotide variant not specified [RCV004482615] Chr6:132693179 [GRCh38]
Chr6:133014318 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.85G>C (p.Val29Leu) single nucleotide variant not specified [RCV004482616] Chr6:132713951 [GRCh38]
Chr6:133035090 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1360G>A (p.Val454Met) single nucleotide variant not specified [RCV004482610] Chr6:132683322 [GRCh38]
Chr6:133004461 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1333A>C (p.Asn445His) single nucleotide variant not specified [RCV004482609] Chr6:132684361 [GRCh38]
Chr6:133005500 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1375C>T (p.Arg459Cys) single nucleotide variant not specified [RCV004688639] Chr6:132683307 [GRCh38]
Chr6:133004446 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.609T>G (p.Phe203Leu) single nucleotide variant not specified [RCV004683126] Chr6:132693241 [GRCh38]
Chr6:133014380 [GRCh37]
Chr6:6q23.2		 uncertain significance
NM_004666.3(VNN1):c.1366A>G (p.Thr456Ala) single nucleotide variant not specified [RCV004688640] Chr6:132683316 [GRCh38]
Chr6:133004455 [GRCh37]
Chr6:6q23.2		 uncertain significance
NC_000006.11:g.(?_131894423)_(133849943_?)del deletion not provided [RCV004578838] Chr6:131894423..133849943 [GRCh37]
Chr6:6q23.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:531
Count of miRNA genes:431
Interacting mature miRNAs:461
Transcripts:ENST00000367928
Prediction methods:Miranda, Rnahybrid
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
407193765GWAS842741_Hlipid measurement QTL GWAS842741 (human)0.000005lipid measurementblood lipid measurement (CMO:0000050)6132711529132711530Human
407178049GWAS827025_Hblood protein measurement QTL GWAS827025 (human)4e-15blood protein measurementblood protein measurement (CMO:0000028)6132695903132695904Human
407241426GWAS890402_Hazelaoyltaurine measurement QTL GWAS890402 (human)8e-23azelaoyltaurine measurement6132701058132701059Human
407177920GWAS826896_Hblood protein measurement QTL GWAS826896 (human)2e-15blood protein measurementblood protein measurement (CMO:0000028)6132695903132695904Human
407209907GWAS858883_Hblood protein measurement QTL GWAS858883 (human)4e-17blood protein measurementblood protein measurement (CMO:0000028)6132695903132695904Human
407193459GWAS842435_Hlipid measurement QTL GWAS842435 (human)3e-13lipid measurementblood lipid measurement (CMO:0000050)6132711529132711530Human
407082298GWAS731274_Hblood protein measurement QTL GWAS731274 (human)1e-18blood protein measurementblood protein measurement (CMO:0000028)6132695903132695904Human
406960824GWAS609800_Hprotein measurement QTL GWAS609800 (human)2e-41protein measurement6132711472132711473Human
407191390GWAS840366_Hlipid measurement QTL GWAS840366 (human)0.000003lipid measurementblood lipid measurement (CMO:0000050)6132694467132694468Human

Markers in Region
VNN1  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376133,014,417 - 133,015,191UniSTSGRCh37
Celera6133,761,242 - 133,762,016UniSTS
HuRef6130,589,336 - 130,590,110UniSTS


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
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2390 2775 2225 4551 1706 2239 4 621 1734 464 2048 7001 6224 30 3524 827 1675 1507 172 1

Sequence


Ensembl Acc Id: ENST00000367928   ⟹   ENSP00000356905
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6132,680,849 - 132,714,055 (-)Ensembl
RefSeq Acc Id: NM_004666   ⟹   NP_004657
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386132,680,849 - 132,714,055 (-)NCBI
GRCh376133,001,997 - 133,035,194 (-)ENTREZGENE
Build 366133,044,422 - 133,076,881 (-)NCBI Archive
HuRef6130,576,916 - 130,610,106 (-)ENTREZGENE
CHM1_16133,265,672 - 133,298,869 (-)NCBI
T2T-CHM13v2.06133,875,818 - 133,909,022 (-)NCBI
Sequence:
RefSeq Acc Id: NP_004657   ⟸   NM_004666
- Peptide Label: precursor
- UniProtKB: Q9UF16 (UniProtKB/Swiss-Prot),   Q4VAS9 (UniProtKB/Swiss-Prot),   Q4VAS8 (UniProtKB/Swiss-Prot),   Q4VAS7 (UniProtKB/Swiss-Prot),   Q4JFW6 (UniProtKB/Swiss-Prot),   A8K310 (UniProtKB/Swiss-Prot),   Q9UJF4 (UniProtKB/Swiss-Prot),   O95497 (UniProtKB/Swiss-Prot),   B2RAN2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000356905   ⟸   ENST00000367928
Protein Domains
CN hydrolase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O95497-F1-model_v2 AlphaFold O95497 1-513 view protein structure

Promoters
RGD ID:7209173
Promoter ID:EPDNEW_H10332
Type:multiple initiation site
Name:VNN1_1
Description:vanin 1
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
GRCh386132,714,055 - 132,714,115EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:12705 AgrOrtholog
COSMIC VNN1 COSMIC
Ensembl Genes ENSG00000112299 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000367928 ENTREZGENE
  ENST00000367928.5 UniProtKB/Swiss-Prot
Gene3D-CATH 3.60.110.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000112299 GTEx
HGNC ID HGNC:12705 ENTREZGENE
Human Proteome Map VNN1 Human Proteome Map
InterPro Biotinidase-like_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotinidase/VNN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-N_Hydrolase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-N_Hydrolase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vanin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:8876 UniProtKB/Swiss-Prot
NCBI Gene 8876 ENTREZGENE
OMIM 603570 OMIM
PANTHER BIOTINIDASE-RELATED UniProtKB/TrEMBL
  PANTETHEINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10609 UniProtKB/Swiss-Prot
Pfam CN_hydrolase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vanin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA37321 PharmGKB
PIRSF Biotinidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CN_HYDROLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Carbon-nitrogen hydrolase UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A8K310 ENTREZGENE
  B2RAN2 ENTREZGENE, UniProtKB/TrEMBL
  O95497 ENTREZGENE
  Q4JFW6 ENTREZGENE
  Q4VAS7 ENTREZGENE
  Q4VAS8 ENTREZGENE
  Q4VAS9 ENTREZGENE
  Q9UF16 ENTREZGENE
  Q9UJF4 ENTREZGENE
  VNN1_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary A8K310 UniProtKB/Swiss-Prot
  Q4JFW6 UniProtKB/Swiss-Prot
  Q4VAS7 UniProtKB/Swiss-Prot
  Q4VAS8 UniProtKB/Swiss-Prot
  Q4VAS9 UniProtKB/Swiss-Prot
  Q9UF16 UniProtKB/Swiss-Prot
  Q9UJF4 UniProtKB/Swiss-Prot