Pi4k2a Gene Detail

Summary

• Symbol
  Pi4k2a
• Name
  phosphatidylinositol 4-kinase type 2 alpha

• Feature Type
  protein coding gene
• IDs
  MGI:1934031
  NCBI Gene: 84095
• Alliance
  gene page
• Transcription Start Sites
  6 TSS
• Candidate for QTL
  6 QTL

Location &
Maps

• Sequence Map
  Chr19:42078909-42110526 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 19, 35.74 cM
• Mapping Data
  6 experiments

Strain
Comparison

• SNPs within 2kb
  1044 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1934031	protein coding gene	Chr19:42078590-42110657 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0025139	protein coding gene	Chr19:41407064-41441106 (+)
A/J	MGP_AJ_G0025116	protein coding gene	Chr19:39416164-39448564 (+)
AKR/J	MGP_AKRJ_G0025084	protein coding gene	Chr19:40707976-40741199 (+)
BALB/cJ	MGP_BALBcJ_G0025110	protein coding gene	Chr19:39482641-39515715 (+)
C3H/HeJ	MGP_C3HHeJ_G0024870	protein coding gene	Chr19:40857435-40888854 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0025553	protein coding gene	Chr19:42470776-42509077 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022967	protein coding gene	Chr19:38770656-38803280 (+)
CAST/EiJ	MGP_CASTEiJ_G0024335	protein coding gene	Chr19:40535848-40570895 (+)
CBA/J	MGP_CBAJ_G0024850	protein coding gene	Chr19:44554782-44586059 (+)
DBA/2J	MGP_DBA2J_G0024982	protein coding gene	Chr19:39265429-39297209 (+)
FVB/NJ	MGP_FVBNJ_G0024943	protein coding gene	Chr19:39039624-39070910 (+)
LP/J	MGP_LPJ_G0025068	protein coding gene	Chr19:41394350-41427731 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024974	protein coding gene	Chr19:44173282-44208873 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025611	protein coding gene	Chr19:40747945-40782824 (+)
PWK/PhJ	MGP_PWKPhJ_G0024084	protein coding gene	Chr19:39143381-39175753 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023888	protein coding gene	Chr19:39494419-39525586 (+)
WSB/EiJ	MGP_WSBEiJ_G0024405	protein coding gene	Chr19:40902275-40936185 (+)

Homology

• Human Ortholog
  PI4K2A, phosphatidylinositol 4-kinase type 2 alpha

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PI4K2A, phosphatidylinositol 4-kinase type 2 alpha
  
• Synonyms
  NEDMSB, PI4KII, PIK42A
• Links
  HGNC:30031

  NCBI Gene ID: 55361

  neXtProt AC: NX_Q9BTU6

  UniProt: Q9BTU6

  
  
• Chr Location
  10q24.2; chr10:97640671-97676434 (+)  GRCh38

---

• MGI Vertebrate Homology
  Pi4k2a stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: PI4K2A
• Gene Tree
  Pi4k2a
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  16 phenotypes from 1 allele in 1 genetic background
  4 images
  11 phenotype references
  

• All Mutations and Alleles
  14
• Endonuclease-mediated
  1
• Gene trapped
  12
• Targeted
  1
• Incidental Mutations
  APF
• Find Mice (IMSR)
  37 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a gene trap allele develop a progressive neurologic disease typified by urinary incontinence, tremor, limb weakness, weight loss, cerebellar gliosis, Purkinje cell loss, degeneration of spinal cord axons and premature death. Mutant males are sterile while females are subfertile.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  55
• GO References
  7

Expression

• Assay Results
  816
• Tissues
  108
• cDNA Data
  105
• Literature Summary
  2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase pi4k2a
  ZFIN pi4k2a

Sequences &
Gene Models

• All Sequences
  60
• RefSeq
  8
• UniProt
  3
• CCDS
  CCDS29821.1

• Ensembl
  ENSMUSG00000025178 (Evidence)
• NCBI Gene
  84095

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000025178	Ensembl Gene Model | MGI Sequence Detail	31618	C57BL/6J
transcript	ENSMUST00000235932	Ensembl | MGI Sequence Detail	1939	Not Applicable
polypeptide	ENSMUSP00000158574	Ensembl | MGI Sequence Detail	479	Not Applicable

Protein
Information

• UniProt
  3 Sequences
• Protein Ontology
  PR:000012681 phosphatidylinositol 4-kinase type 2-alpha
  (term hierarchy)
• EC
  2.7.1.67
• InterPro Domains
  IPR000403 Phosphatidylinositol 3-/4-kinase, catalytic domain
  IPR039756 Type II phosphatidylinositol 4-kinase Lsb6/PI4K2

Molecular
Reagents

• All nucleic 106

  cDNA 105

  Primer pair 1

  
  

  Microarray probesets 5

References

• Summaries
  All 47

  Developmental Gene Expression 2

  Gene Ontology 7

  Phenotypes 11
• Earliest
  J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
• Latest
  J:315200 Khundadze M, et al., Mouse models for hereditary spastic paraplegia uncover a role of PI4K2A in autophagic lysosome reformation. Autophagy. 2021 Nov;17(11):3690-3706

TSS for Pi4k2a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr156478	Chr19:42078861-42078941 (+)	-8 bp
Tssr156479	Chr19:42078955-42078971 (+)	54 bp
Tssr156480	Chr19:42079983-42079996 (+)	1,081 bp
Tssr156481	Chr19:42094600-42094619 (+)	15,701 bp
Tssr156482	Chr19:42105999-42106003 (+)	27,092 bp
Tssr156483	Chr19:42108668-42108706 (+)	29,778 bp

Pi4k2a is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Afw8	Chr19, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Bglq13	Chr19, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Iba4	Chr19, 20.99 cM	Chr19:26305715-26305821	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Nobq2	Chr19, 40.53 cM	Chr19:47897880-47897988	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
T2dm2	Chr19, 50.72 cM	Chr19:55376050-55376167	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Tanidd1	Chr19, 48.46 cM	Chr19:53752597-53752718	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.

*cM position of peak correlated region/marker