PKDCC protein kinase domain containing, cytoplasmic [Homo sapiens (human)] - Gene

Summary

Official Symbol: PKDCCprovided by HGNC
Official Full Name: protein kinase domain containing, cytoplasmicprovided by HGNC
Primary source: HGNC:HGNC:25123
See related: Ensembl:ENSG00000162878 MIM:614150; AllianceGenome:HGNC:25123
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: Vlk; RLSDF; SGK493
Summary: Enables non-membrane spanning protein tyrosine kinase activity. Involved in peptidyl-tyrosine phosphorylation and skeletal system development. Located in extracellular region. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in ovary (RPKM 28.2), endometrium (RPKM 26.6) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p21

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (42048021..42058517)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (42053518..42064014)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (42275161..42285657)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1.
Title: Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1.
A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis.
Title: A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis.
Prenatal diagnosis to identify compound heterozygous variants in PKDCC that causes rhizomelic limb shortening with dysmorphic features in a fetus from China.
Title: Prenatal diagnosis to identify compound heterozygous variants in PKDCC that causes rhizomelic limb shortening with dysmorphic features in a fetus from China.
The prevalence and phenotypic range associated with biallelic PKDCC variants.
Title: The prevalence and phenotypic range associated with biallelic PKDCC variants.
The secreted tyrosine kinase VLK is essential for normal platelet activation and thrombus formation.
Title: The secreted tyrosine kinase VLK is essential for normal platelet activation and thrombus formation.
Taken together, these results suggest that Vlk may function as a signaling regulator in extracellular space to modulate the Hedgehog pathway
Title: Secreted tyrosine kinase Vlk negatively regulates Hedgehog signaling by inducing lysosomal degradation of Smoothened.
Each patient had a homozygous gene disrupting variant in PKDCC considered to explain the skeletal phenotypes shared by both.
Title: Biallelic disruption of PKDCC is associated with a skeletal disorder characterised by rhizomelic shortening of extremities and dysmorphic features.
VLK secretion can be regulated by external cues, intracellular signal proteins, and mechanical stretch, and VLK can in turn regulate TyrP of ECM proteins secreted by trabecular meshwork cells and control cell shape, actin stress fibers, and focal adhesions.
Title: Vertebrate Lonesome Kinase Regulated Extracellular Matrix Protein Phosphorylation, Cell Shape, and Adhesion in Trabecular Meshwork Cells.
The Fam20C-and VLK-family of kinases mediate the phosphorylation of proteins in the secretory pathway and extracellular space.Mutation in several secretory pathway kinases cause human disease
Title: The secretory pathway kinases.
VLK is rapidly and quantitatively secreted from platelets in response to stimuli and can tyrosine phosphorylate coreleased proteins utilizing endogenous as well as exogenous ATP sources.
Title: A secreted tyrosine kinase acts in the extracellular environment.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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

Associated conditions

Description	Tests
Rhizomelic limb shortening with dysmorphic features MedGen: C5394173 OMIM: 618821 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS). EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analyses identify variants in developmental genes associated with hypospadias. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:486914

WI-15430 (e-PCR)
- UniSTS:15166

A004O39 (e-PCR)
- UniSTS:3936

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables histone H2AXY142 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3Y41 kinase activity	IEA Inferred from Electronic Annotation more info
enables non-membrane spanning protein tyrosine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables non-membrane spanning protein tyrosine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein kinase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in bone mineralization	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in embryonic digestive tract development	ISS Inferred from Sequence or Structural Similarity more info
involved_in limb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in lung alveolus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of Golgi to plasma membrane protein transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of bone mineralization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of chondrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in roof of mouth development	ISS Inferred from Sequence or Structural Similarity more info
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in extracellular region	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: extracellular tyrosine-protein kinase PKDCC

Names: protein kinase domain containing, cytoplasmic homolog; protein kinase domain-containing protein, cytoplasmic; protein kinase-like protein SgK493; sugen kinase 493; vertebrate lonesome kinase

NP_612379.2

EC 2.7.10.2

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.