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ITFG2 integrin alpha FG-GAP repeat containing 2 [ Homo sapiens (human) ]

Gene ID: 55846, updated on 3-Nov-2024

Summary

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Official Symbol
ITFG2provided by HGNC
Official Full Name
integrin alpha FG-GAP repeat containing 2provided by HGNC
Primary source
HGNC:HGNC:30879
See related
Ensembl:ENSG00000111203 MIM:617421; AllianceGenome:HGNC:30879
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KICS3; FGGAP1; MDS028
Summary
Involved in cellular response to amino acid starvation; cellular response to glucose starvation; and negative regulation of TORC1 signaling. Located in Golgi apparatus and lysosomal membrane. Part of KICSTOR complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 9.5), ovary (RPKM 9.0) and 25 other tissues See more
Orthologs
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Genomic context

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See ITFG2 in Genome Data Viewer
Location:
12p13.33
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (2812668..2859791)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (2818668..2865802)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (2921834..2968957)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ITFG2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2903015-2903560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2903561-2904105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4132 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:2905599-2906798 Neighboring gene CBX3 pseudogene 4 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:2921381-2922130 Neighboring gene FKBP prolyl isomerase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2928702-2929202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2929203-2929703 Neighboring gene Sharpr-MPRA regulatory region 8339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2943338-2943882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2943883-2944427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2944428-2944971 Neighboring gene nuclear receptor interacting protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2953993-2954980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2954981-2955966 Neighboring gene testis expressed 52 Neighboring gene forkhead box M1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4135 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2988229-2989182 Neighboring gene uncharacterized LOC124902860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4136 Neighboring gene RAD9-HUS1-RAD1 interacting nuclear orphan 1 Neighboring gene TUB like protein 3 Neighboring gene Sharpr-MPRA regulatory region 7040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3032139-3032645 Neighboring gene U7 small nuclear RNA

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1. Wolfson RL, et al. Nature, 2017 Mar 16. PMID 28199306, Free PMC Article
  2. Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality. Navare AT, et al. J Cell Biol, 2022 Nov 7. PMID 36305789, Free PMC Article
  3. A "double adaptor" method for improved shotgun library construction. Andersson B, et al. Anal Biochem, 1996 Apr 5. PMID 8619474
  4. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Yang X, et al. Cell, 2016 Feb 11. PMID 26871637, Free PMC Article
  5. Large-scale mapping of human protein-protein interactions by mass spectrometry. Ewing RM, et al. Mol Syst Biol, 2007. PMID 17353931, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cellular response to amino acid starvation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to glucose starvation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in germinal center B cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of TORC1 signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of TOR signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
part_of KICSTOR complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of KICSTOR complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of KICSTOR complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
KICSTOR complex protein ITFG2
Names
FG-GAP repeat containing 1
integrin-alpha FG-GAP repeat-containing protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_018463.4 → NP_060933.3  KICSTOR complex protein ITFG2

    See identical proteins and their annotated locations for NP_060933.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes a functional protein.
    Source sequence(s)
    AC005841, BC013399, BQ003916, BQ058412
    Consensus CDS
    CCDS8513.1
    UniProtKB/Swiss-Prot
    A8K4Z5, D3DUQ2, Q6PKU5, Q969R8, Q96SX6
    UniProtKB/TrEMBL
    A0A0S2Z5G6, A0A0S2Z5P1
    Related
    ENSP00000228799.2, ENST00000228799.7
    Conserved Domains (2) summary
    pfam15907
    Location:49 → 386
    Itfg2; Integrin-alpha FG-GAP repeat-containing protein 2
    cl24051
    Location:22 → 53
    BBS2_Mid; Ciliary BBSome complex subunit 2, middle region

RNA

  1. NR_130744.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in an internal exon and an alternate 3' terminal sequence, compared to variant 1. This variant is represented as non-coding because the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005841, AK027483, AK300905, BQ058412

  2. NR_147202.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005841, AW151238
    Related
    ENST00000645513.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    2812668..2859791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    2818668..2865802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_038933.1: Suppressed sequence

    Description
    NR_038933.1: This RefSeq was removed because it is now thought that this transcript is partial.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969R8.1 GenPept UniProtKB/Swiss-Prot:Q969R8

Gene LinkOut

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