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KNDC1 kinase non-catalytic C-lobe domain containing 1 [ Homo sapiens (human) ]

Gene ID: 85442, updated on 3-Apr-2024

Summary

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Official Symbol
KNDC1provided by HGNC
Official Full Name
kinase non-catalytic C-lobe domain containing 1provided by HGNC
Primary source
HGNC:HGNC:29374
See related
Ensembl:ENSG00000171798 MIM:616237; AllianceGenome:HGNC:29374
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
v-KIND; RASGEF2; C10orf23; Very-KIND; bB439H18.3
Summary
The protein encoded by this gene is a Ras guanine nucleotide exchange factor that appears to negatively regulate dendritic growth in the brain. Knockdown of this gene in senescent umbilical vein endothelial cells partially reversed the senescence, showing that this gene could potentially be targeted by anti-aging therapies. [provided by RefSeq, Dec 2016]
Expression
Biased expression in brain (RPKM 6.5), ovary (RPKM 2.2) and 6 other tissues See more
Orthologs
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Genomic context

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Location:
10q26.3
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (133160219..133226412)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (134116905..134181903)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (134973723..135039916)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134902582-134903344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134911870-134912370 Neighboring gene adhesion G protein-coupled receptor A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134915449-134916424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134917665-134918227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134918228-134918789 Neighboring gene CEB36 minisatellite repeat instability region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134940316-134941027 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134941028-134941740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134953797-134954355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134963792-134964598 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134964599-134965404 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134965405-134966211 Neighboring gene ribosomal protein L5 pseudogene 28 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134974094-134974683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134974684-134975274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134979051-134979562 Neighboring gene uncharacterized LOC105378574 Neighboring gene uncharacterized LOC105378573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135013107-135013853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135013854-135014599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135038599-135039222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:135043703-135044502 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135045303-135046102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135048520-135049124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135050334-135050937 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135050938-135051542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135051543-135052146 Neighboring gene undifferentiated embryonic cell transcription factor 1 Neighboring gene VENT homeobox

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
  • 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. Effect of KNDC1 overexpression on the senescence of human umbilical vein endothelial cells. Ji J, et al. Mol Med Rep, 2018 May. PMID 29568929, Free PMC Article
  2. KNDC1 knockdown protects human umbilical vein endothelial cells from senescence. Zhang C, et al. Mol Med Rep, 2014 Jul. PMID 24788352, Free PMC Article
  3. The brain-specific RasGEF very-KIND is required for normal dendritic growth in cerebellar granule cells and proper motor coordination. Hayashi K, et al. PLoS One, 2017. PMID 28264072, Free PMC Article
  4. Progesterone induced Warburg effect in HEK293 cells is associated with post-translational modifications and proteasomal degradation of progesterone receptor membrane component 1. Sabbir MG. J Steroid Biochem Mol Biol, 2019 Jul. PMID 31067491
  5. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Dec 31. PMID 11214970

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The results demonstrated that KNDC1 overexpression possibly inhibited HUVEC activity and function and promoted HUVEC senescence. Mechanistic studies demonstrated that KNDC1 triggered a p53ROS positive feedback loop, which serves a crucial role in regulating senescence.
    Title: Effect of KNDC1 overexpression on the senescence of human umbilical vein endothelial cells.
  2. KNDC1 knockdown promoted HUVEC proliferation via the extracellular signal-regulated kinase signaling pathway and delayed HUVEC senescence by inhibiting the p53-p21-p16 transduction cascade.
    Title: KNDC1 knockdown protects human umbilical vein endothelial cells from senescence.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
Submit: New GeneRIF Correction

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ16067

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in cerebellar granule cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of dendrite morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in small GTPase-mediated signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of guanyl-nucleotide exchange factor complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of guanyl-nucleotide exchange factor complex ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perikaryon IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
kinase non-catalytic C-lobe domain-containing protein 1
Names
KIND domain-containing protein 1
RasGEF domain family, member 2
cerebral protein 9
kinase non-catalytic C-lobe domain (KIND) containing 1
protein very KIND
ras-GEF domain-containing family member 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.

Genomic

  1. NG_053178.1 RefSeqGene

    Range
    5124..71317
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001347864.2 → NP_001334793.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL445199
    Consensus CDS
    CCDS91390.1
    UniProtKB/TrEMBL
    A0A804HIZ4
    Related
    ENSP00000507288.1, ENST00000684739.1

  2. NM_001347865.2 → NP_001334794.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL445199
    Consensus CDS
    CCDS91388.1
    UniProtKB/TrEMBL
    A0A804HID6, A0A804HKF6
    Related
    ENSP00000507020.1, ENST00000682765.1

  3. NM_001347866.2 → NP_001334795.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL445199
    Consensus CDS
    CCDS91389.1
    UniProtKB/TrEMBL
    A0A804HHZ0, A0A804HKF6
    Related
    ENSP00000506821.1, ENST00000683259.1
    Conserved Domains (1) summary
    cl21453
    Location:37 → 120
    PKc_like; Protein Kinases, catalytic domain

  4. NM_152643.8 → NP_689856.6  kinase non-catalytic C-lobe domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_689856.6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL445199
    Consensus CDS
    CCDS7674.1
    UniProtKB/Swiss-Prot
    B0QZC5, Q5T233, Q6ZNH8, Q76NI1, Q8TEE5, Q96LV7, Q9C095
    Related
    ENSP00000304437.3, ENST00000304613.8
    Conserved Domains (5) summary
    cd06224
    Location:1254 → 1368
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    smart00750
    Location:37 → 217
    KIND; kinase non-catalytic C-lobe domain
    pfam00617
    Location:1475 → 1673
    RasGEF; RasGEF domain
    pfam15760
    Location:215 → 333
    DLEU7; Leukemia-associated protein 7
    cl21453
    Location:444 → 608
    PKc_like; Protein Kinases, catalytic domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    133160219..133226412
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016858.3 → XP_016872347.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X1

    Conserved Domains (5) summary
    cd06224
    Location:1254 → 1368
    REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
    smart00750
    Location:37 → 217
    KIND; kinase non-catalytic C-lobe domain
    PHA03247
    Location:619 → 896
    PHA03247; large tegument protein UL36; Provisional
    pfam00617
    Location:1475 → 1560
    RasGEF; RasGEF domain
    cl21453
    Location:444 → 608
    PKc_like; Protein Kinases, catalytic domain

  2. XM_017016859.3 → XP_016872348.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    A0A7I2PM36
    Related
    ENSP00000507504.1, ENST00000684081.1
    Conserved Domains (3) summary
    smart00750
    Location:37 → 217
    KIND; kinase non-catalytic C-lobe domain
    PHA03247
    Location:619 → 896
    PHA03247; large tegument protein UL36; Provisional
    cl21453
    Location:444 → 608
    PKc_like; Protein Kinases, catalytic domain

  3. XM_024448245.2 → XP_024304013.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A804HI34, A0A804HKF6
    Related
    ENSP00000506878.1, ENST00000478074.6
    Conserved Domains (1) summary
    cl21453
    Location:37 → 132
    PKc_like; Protein Kinases, catalytic domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    134116905..134181903
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367052.1 → XP_054223027.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X1

  2. XM_054367053.1 → XP_054223028.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X2

  3. XM_054367054.1 → XP_054223029.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A804HI34
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q76NI1.2 GenPept UniProtKB/Swiss-Prot:Q76NI1

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