Gene: Vax1

Basic information

Tag Content
Uniprot ID Q2NKI2; O88880;
Entrez ID 22326
Genbank protein ID BAA76866.1; AAI11819.1; AAC36319.1;
Genbank nucleotide ID NM_009501.2
Ensembl protein ID ENSMUSP00000134642
Ensembl nucleotide ID ENSMUSG00000006270
Gene name Ventral anterior homeobox 1
Gene symbol Vax1
Organism Mus musculus
NCBI taxa ID 10090
Cleft type CPO
Developmental stage
Data sources Manually collected
Reference 10601035; 15905411;
Functional description Transcription factor that may function in dorsoventral specification of the forebrain. Required for axon guidance and major tract formation in the developing forebrain. May contribute to the differentiation of the neuroretina, pigmented epithelium and optic stalk.
Sequence
MFGKPDKMDV RCHSDTEAAR VSKNAHKESR EIKGAEGSLP AAFLKEPQGA FSGSGASEDC 60
NKSKSNSSAD PDYCRRILVR DAKGSIREII LPKGLDLDRP KRTRTSFTAE QLYRLEMEFQ 120
RCQYVVGRER TELARQLNLS ETQVKVWFQN RRTKQKKDQG KDSELRSVVS ETAATCSVLR 180
LLEQGRLLSP PGLPALLPPC ATGALGSALR GPSLPALGAG AAAGSAAAAA AAAAATAPGP 240
AGAASQHQPA VGGAPGPGPA GPGGLHAGAP TASHGLFSLP VPSLLGSVAS RLSSAPLTMA 300
GSLAGNLQEL SARYLSSSAF EPYSRTNNKE GAEKKALD 338

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation Gene symbol Entrez ID UniProt ID Cleft type Developmental stage Species Evidence Details
1:1 orthologVAX1486906E2QUC0Canis lupus familiarisPredictionMore>>
1:1 orthologVAX1102190017A0A452DMM9Capra hircusPredictionMore>>
1:1 orthologVAX111023Q5SQQ9CL/PHomo sapiensPublicationMore>>
1:1 orthologVax122326Q2NKI2CPOMus musculusPublicationMore>>
1:1 orthologVAX1740057A0A2I3TJG6Pan troglodytesPredictionMore>>
1:1 orthologVAX1100157019F1S4S0Sus scrofaPredictionMore>>
1:1 orthologVax164571Q9JM00Rattus norvegicusPredictionMore>>
1:1 orthologvax1373870A0A0R4I9B5Danio rerioPredictionMore>>

Identified variants/mutations related to cleft phenotype

Gene symbol Significant Variants/SNPS Methods PubMed ID
VAX1c.453_454delinsAA; p.Arg152SerPCR; sequencing22095910
VAX1c.945C>T; p.Ala315AlaPCR; sequencing22095910
VAX1rs4752028 Genotyping; direct sequencing; and TDT23463464
VAX1rs7078160 Genotyping; direct sequencing; and TDT23463464
VAX1rs14874160G>T Genotyping; direct sequencing; and TDT23463464
VAX1c.898982>C Genotyping; direct sequencing; and TDT23463464
VAX1rs148741605C>T Genotyping; direct sequencing; and TDT23463464
VAX1c.840949G>A Genotyping; direct sequencing; and TDT23463464
VAX1c.840439C>A Genotyping; direct sequencing; and TDT23463464
VAX1c.897839C>T Genotyping; direct sequencing; and TDT23463464
VAX1c.896171G>T Genotyping; direct sequencing; and TDT23463464
VAX1c.896062T>G; p.M117R Genotyping; direct sequencing; and TDT23463464
VAX1c.893947C>T Genotyping; direct sequencing; and TDT23463464
VAX1c.893882G>T Genotyping; direct sequencing; and TDT23463464
VAX1c.893824G>T; p.A233S Genotyping; direct sequencing; and TDT23463464
VAX1rs7902527G>AGWAS31609978
VAX1rs4752028T>CGWAS31609978
VAX1rs4752028C>Trealtime-PCR30633559
VAX1rs7078160G>A (increasing risk)realtime-PCR30633559
VAX1rs6585429A>GGWAS28232668
VAX1rs7078160G>A (increasing risk)SNPscan method and TDT30048854
VAX1rs7078160G>A (increasing risk)PCR and Sanger sequencing33132092
VAX1rs7086344*TGenotyping26602496
VAX1rs10886040Genotyping and GWAS27033726
VAX1rs201128098Genotyping and GWAS27033726
VAX1rs7072663Genotyping and GWAS27033726
VAX1rs113339720Genotyping and GWAS27033726

Other genetic variants/mutations

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID GO Term Evidence
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA bindingIBA
GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA bindingIDA
GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA bindingIBA
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specificIDA
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specificIBA
GO:0003700 DNA-binding transcription factor activityIMP
GO:0031490 chromatin DNA bindingIDA

GO:Biological Process

GO ID GO Term Evidence
GO:0000122 negative regulation of transcription by RNA polymerase IIIDA
GO:0000122 negative regulation of transcription by RNA polymerase IIIGI
GO:0001764 neuron migrationIMP
GO:0006357 regulation of transcription by RNA polymerase IIIBA
GO:0007399 nervous system developmentIMP
GO:0007406 negative regulation of neuroblast proliferationIMP
GO:0007411 axon guidanceIMP
GO:0007417 central nervous system developmentIMP
GO:0007417 central nervous system developmentIBA
GO:0007420 brain developmentIMP
GO:0030154 cell differentiationIMP
GO:0030182 neuron differentiationIBA
GO:0035914 skeletal muscle cell differentiationIMP
GO:0043010 camera-type eye developmentIGI
GO:0060021 roof of mouth developmentIMP

GO:Cellular Component

GO ID GO Term Evidence
GO:0005634 nucleusIDA
GO:0005634 nucleusIBA

Reactome Pathway

Reactome ID Reactome Term Evidence

Functional annotations

Keywords

Keyword ID Keyword Term
KW-0025 Alternative splicing
KW-0217 Developmental protein
KW-0238 DNA-binding
KW-0371 Homeobox
KW-0539 Nucleus
KW-1185 Reference proteome
KW-0804 Transcription
KW-0805 Transcription regulation

Interpro

InterPro ID InterPro Term
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR000047 HTH_motif
IPR033020 Vax1

PROSITE

PROSITE ID PROSITE Term
PS00027 HOMEOBOX_1
PS50071 HOMEOBOX_2

Pfam

Pfam ID Pfam Term
PF00046 Homeodomain