Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	91461
Gene name	Protein kinase domain containing, cytoplasmic
Gene symbol	PKDCC
Synonyms (NCBI Gene)	RLSDFSGK493Vlk
Chromosome	2
Chromosome location	2p21

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs761532715	C>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs763243200	G>A,T	Pathogenic, likely-pathogenic	Splice donor variant

186

Show/Hide all (186)

miRTarBase ID	miRNA	Experiments	Reference
MIRT050335	hsa-miR-25-3p	CLASH	23622248
MIRT049360	hsa-miR-92a-3p	CLASH	23622248
MIRT1237321	hsa-miR-103a	CLIP-seq
MIRT1237322	hsa-miR-107	CLIP-seq
MIRT1237323	hsa-miR-1256	CLIP-seq
MIRT1237324	hsa-miR-1271	CLIP-seq
MIRT1237325	hsa-miR-1304	CLIP-seq
MIRT1237326	hsa-miR-1321	CLIP-seq
MIRT1237327	hsa-miR-1343	CLIP-seq
MIRT1237328	hsa-miR-137	CLIP-seq
MIRT1237329	hsa-miR-15a	CLIP-seq
MIRT1237330	hsa-miR-15b	CLIP-seq
MIRT1237331	hsa-miR-16	CLIP-seq
MIRT1237332	hsa-miR-182	CLIP-seq
MIRT1237333	hsa-miR-1827	CLIP-seq
MIRT1237334	hsa-miR-1909	CLIP-seq
MIRT1237335	hsa-miR-1915	CLIP-seq
MIRT1237336	hsa-miR-195	CLIP-seq
MIRT1237337	hsa-miR-214	CLIP-seq
MIRT1237338	hsa-miR-2355-3p	CLIP-seq
MIRT1237339	hsa-miR-23a	CLIP-seq
MIRT1237340	hsa-miR-23b	CLIP-seq
MIRT1237341	hsa-miR-23c	CLIP-seq
MIRT1237342	hsa-miR-2467-5p	CLIP-seq
MIRT1237343	hsa-miR-25	CLIP-seq
MIRT1237344	hsa-miR-28-5p	CLIP-seq
MIRT1237345	hsa-miR-3120-5p	CLIP-seq
MIRT1237346	hsa-miR-3139	CLIP-seq
MIRT1237347	hsa-miR-3143	CLIP-seq
MIRT1237348	hsa-miR-3184	CLIP-seq
MIRT1237349	hsa-miR-3188	CLIP-seq
MIRT1237350	hsa-miR-32	CLIP-seq
MIRT1237351	hsa-miR-3619-5p	CLIP-seq
MIRT1237352	hsa-miR-363	CLIP-seq
MIRT1237353	hsa-miR-367	CLIP-seq
MIRT1237354	hsa-miR-3690	CLIP-seq
MIRT1237355	hsa-miR-378	CLIP-seq
MIRT1237356	hsa-miR-378b	CLIP-seq
MIRT1237357	hsa-miR-378c	CLIP-seq
MIRT1237358	hsa-miR-378d	CLIP-seq
MIRT1237359	hsa-miR-378e	CLIP-seq
MIRT1237360	hsa-miR-378f	CLIP-seq
MIRT1237361	hsa-miR-378h	CLIP-seq
MIRT1237362	hsa-miR-378i	CLIP-seq
MIRT1237363	hsa-miR-3943	CLIP-seq
MIRT1237364	hsa-miR-3944-5p	CLIP-seq
MIRT1237365	hsa-miR-3975	CLIP-seq
MIRT1237366	hsa-miR-422a	CLIP-seq
MIRT1237367	hsa-miR-423-5p	CLIP-seq
MIRT1237368	hsa-miR-424	CLIP-seq
MIRT1237369	hsa-miR-4254	CLIP-seq
MIRT1237370	hsa-miR-4270	CLIP-seq
MIRT1237371	hsa-miR-4274	CLIP-seq
MIRT1237372	hsa-miR-4441	CLIP-seq
MIRT1237373	hsa-miR-4530	CLIP-seq
MIRT1237374	hsa-miR-4642	CLIP-seq
MIRT1237375	hsa-miR-4646-3p	CLIP-seq
MIRT1237376	hsa-miR-4688	CLIP-seq
MIRT1237377	hsa-miR-4707-5p	CLIP-seq
MIRT1237378	hsa-miR-4726-3p	CLIP-seq
MIRT1237379	hsa-miR-4728-5p	CLIP-seq
MIRT1237380	hsa-miR-4739	CLIP-seq
MIRT1237381	hsa-miR-4756-5p	CLIP-seq
MIRT1237382	hsa-miR-4758-3p	CLIP-seq
MIRT1237383	hsa-miR-485-5p	CLIP-seq
MIRT1237384	hsa-miR-488	CLIP-seq
MIRT1237385	hsa-miR-497	CLIP-seq
MIRT1237386	hsa-miR-543	CLIP-seq
MIRT1237387	hsa-miR-676	CLIP-seq
MIRT1237388	hsa-miR-708	CLIP-seq
MIRT1237389	hsa-miR-761	CLIP-seq
MIRT1237390	hsa-miR-92a	CLIP-seq
MIRT1237391	hsa-miR-92b	CLIP-seq
MIRT1237392	hsa-miR-96	CLIP-seq
MIRT1922922	hsa-miR-24	CLIP-seq
MIRT1922923	hsa-miR-4284	CLIP-seq
MIRT1237321	hsa-miR-103a	CLIP-seq
MIRT1237322	hsa-miR-107	CLIP-seq
MIRT1237327	hsa-miR-1343	CLIP-seq
MIRT1237329	hsa-miR-15a	CLIP-seq
MIRT1237330	hsa-miR-15b	CLIP-seq
MIRT1237331	hsa-miR-16	CLIP-seq
MIRT1237334	hsa-miR-1909	CLIP-seq
MIRT1237336	hsa-miR-195	CLIP-seq
MIRT1237337	hsa-miR-214	CLIP-seq
MIRT1237344	hsa-miR-28-5p	CLIP-seq
MIRT1237346	hsa-miR-3139	CLIP-seq
MIRT1237351	hsa-miR-3619-5p	CLIP-seq
MIRT2069856	hsa-miR-3622b-5p	CLIP-seq
MIRT1237354	hsa-miR-3690	CLIP-seq
MIRT1237355	hsa-miR-378	CLIP-seq
MIRT1237356	hsa-miR-378b	CLIP-seq
MIRT1237357	hsa-miR-378c	CLIP-seq
MIRT1237358	hsa-miR-378d	CLIP-seq
MIRT1237359	hsa-miR-378e	CLIP-seq
MIRT1237360	hsa-miR-378f	CLIP-seq
MIRT1237361	hsa-miR-378h	CLIP-seq
MIRT1237362	hsa-miR-378i	CLIP-seq
MIRT2069857	hsa-miR-3929	CLIP-seq
MIRT1237364	hsa-miR-3944-5p	CLIP-seq
MIRT1237366	hsa-miR-422a	CLIP-seq
MIRT1237368	hsa-miR-424	CLIP-seq
MIRT1237369	hsa-miR-4254	CLIP-seq
MIRT1237371	hsa-miR-4274	CLIP-seq
MIRT2069858	hsa-miR-4419b	CLIP-seq
MIRT2069859	hsa-miR-4478	CLIP-seq
MIRT2069860	hsa-miR-4490	CLIP-seq
MIRT1237373	hsa-miR-4530	CLIP-seq
MIRT1237385	hsa-miR-497	CLIP-seq
MIRT2069861	hsa-miR-645	CLIP-seq
MIRT1237388	hsa-miR-708	CLIP-seq
MIRT1237389	hsa-miR-761	CLIP-seq
MIRT1237327	hsa-miR-1343	CLIP-seq
MIRT1237344	hsa-miR-28-5p	CLIP-seq
MIRT1237346	hsa-miR-3139	CLIP-seq
MIRT1237354	hsa-miR-3690	CLIP-seq
MIRT1237355	hsa-miR-378	CLIP-seq
MIRT1237356	hsa-miR-378b	CLIP-seq
MIRT1237357	hsa-miR-378c	CLIP-seq
MIRT1237358	hsa-miR-378d	CLIP-seq
MIRT1237359	hsa-miR-378e	CLIP-seq
MIRT1237360	hsa-miR-378f	CLIP-seq
MIRT1237361	hsa-miR-378h	CLIP-seq
MIRT1237362	hsa-miR-378i	CLIP-seq
MIRT1237366	hsa-miR-422a	CLIP-seq
MIRT1237369	hsa-miR-4254	CLIP-seq
MIRT1237371	hsa-miR-4274	CLIP-seq
MIRT1237373	hsa-miR-4530	CLIP-seq
MIRT1237388	hsa-miR-708	CLIP-seq
MIRT1237334	hsa-miR-1909	CLIP-seq
MIRT2594509	hsa-miR-122	CLIP-seq
MIRT2594510	hsa-miR-1587	CLIP-seq
MIRT2594511	hsa-miR-2355-5p	CLIP-seq
MIRT2594512	hsa-miR-3176	CLIP-seq
MIRT2594513	hsa-miR-3192	CLIP-seq
MIRT2594514	hsa-miR-331-3p	CLIP-seq
MIRT2594515	hsa-miR-339-5p	CLIP-seq
MIRT2594516	hsa-miR-3657	CLIP-seq
MIRT1237354	hsa-miR-3690	CLIP-seq
MIRT2594517	hsa-miR-378g	CLIP-seq
MIRT2594518	hsa-miR-3919	CLIP-seq
MIRT2594519	hsa-miR-3922-3p	CLIP-seq
MIRT1237369	hsa-miR-4254	CLIP-seq
MIRT2594520	hsa-miR-4292	CLIP-seq
MIRT2594521	hsa-miR-4492	CLIP-seq
MIRT2594522	hsa-miR-4498	CLIP-seq
MIRT2594523	hsa-miR-4656	CLIP-seq
MIRT2594524	hsa-miR-4675	CLIP-seq
MIRT1237378	hsa-miR-4726-3p	CLIP-seq
MIRT2594525	hsa-miR-4741	CLIP-seq
MIRT2594526	hsa-miR-4756-3p	CLIP-seq
MIRT2594527	hsa-miR-4793-5p	CLIP-seq
MIRT2594528	hsa-miR-661	CLIP-seq
MIRT2594529	hsa-miR-762	CLIP-seq
MIRT2594509	hsa-miR-122	CLIP-seq
MIRT2687957	hsa-miR-128	CLIP-seq
MIRT1237326	hsa-miR-1321	CLIP-seq
MIRT2594510	hsa-miR-1587	CLIP-seq
MIRT1237335	hsa-miR-1915	CLIP-seq
MIRT2594512	hsa-miR-3176	CLIP-seq
MIRT1237348	hsa-miR-3184	CLIP-seq
MIRT2594513	hsa-miR-3192	CLIP-seq
MIRT2594514	hsa-miR-331-3p	CLIP-seq
MIRT2594515	hsa-miR-339-5p	CLIP-seq
MIRT2594516	hsa-miR-3657	CLIP-seq
MIRT2687958	hsa-miR-3675-5p	CLIP-seq
MIRT2594517	hsa-miR-378g	CLIP-seq
MIRT2594519	hsa-miR-3922-3p	CLIP-seq
MIRT1237367	hsa-miR-423-5p	CLIP-seq
MIRT1237370	hsa-miR-4270	CLIP-seq
MIRT2687959	hsa-miR-4283	CLIP-seq
MIRT2594520	hsa-miR-4292	CLIP-seq
MIRT1237372	hsa-miR-4441	CLIP-seq
MIRT2687960	hsa-miR-4489	CLIP-seq
MIRT2594521	hsa-miR-4492	CLIP-seq
MIRT2594522	hsa-miR-4498	CLIP-seq
MIRT2594523	hsa-miR-4656	CLIP-seq
MIRT2594524	hsa-miR-4675	CLIP-seq
MIRT1237376	hsa-miR-4688	CLIP-seq
MIRT1237378	hsa-miR-4726-3p	CLIP-seq
MIRT1237379	hsa-miR-4728-5p	CLIP-seq
MIRT1237380	hsa-miR-4739	CLIP-seq
MIRT2594525	hsa-miR-4741	CLIP-seq
MIRT1237381	hsa-miR-4756-5p	CLIP-seq
MIRT2594528	hsa-miR-661	CLIP-seq
MIRT2594529	hsa-miR-762	CLIP-seq

Show/Hide all (38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0001501	Process	Skeletal system development	IBA
GO:0001501	Process	Skeletal system development	IEA
GO:0001501	Process	Skeletal system development	IEA
GO:0001501	Process	Skeletal system development	IMP	30478137
GO:0001503	Process	Ossification	IEA
GO:0004672	Function	Protein kinase activity	IEA
GO:0004672	Function	Protein kinase activity	ISS
GO:0004713	Function	Protein tyrosine kinase activity	IEA
GO:0004715	Function	Non-membrane spanning protein tyrosine kinase activity	IBA
GO:0004715	Function	Non-membrane spanning protein tyrosine kinase activity	IDA	25171405
GO:0004715	Function	Non-membrane spanning protein tyrosine kinase activity	IEA
GO:0005524	Function	ATP binding	IEA
GO:0005576	Component	Extracellular region	IBA
GO:0005576	Component	Extracellular region	IDA	25171405
GO:0005576	Component	Extracellular region	IEA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005794	Component	Golgi apparatus	ISS
GO:0015031	Process	Protein transport	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0018108	Process	Peptidyl-tyrosine phosphorylation	IDA	25171405
GO:0030154	Process	Cell differentiation	IEA
GO:0030282	Process	Bone mineralization	IEA
GO:0030501	Process	Positive regulation of bone mineralization	IEA
GO:0030501	Process	Positive regulation of bone mineralization	ISS
GO:0032332	Process	Positive regulation of chondrocyte differentiation	IEA
GO:0032332	Process	Positive regulation of chondrocyte differentiation	ISS
GO:0035108	Process	Limb morphogenesis	IEA
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042997	Process	Negative regulation of Golgi to plasma membrane protein transport	IEA
GO:0042997	Process	Negative regulation of Golgi to plasma membrane protein transport	ISS
GO:0048286	Process	Lung alveolus development	IEA
GO:0048286	Process	Lung alveolus development	ISS
GO:0048566	Process	Embryonic digestive tract development	IEA
GO:0048566	Process	Embryonic digestive tract development	ISS
GO:0060021	Process	Roof of mouth development	IEA
GO:0060021	Process	Roof of mouth development	ISS

MIM	HGNC	e!Ensembl
614150	25123	ENSG00000162878

Q504Y2

Protein name

Extracellular tyrosine-protein kinase PKDCC (EC 2.7.10.2) (Protein kinase domain-containing protein, cytoplasmic) (Protein kinase-like protein SgK493) (Sugen kinase 493) (Vertebrate lonesome kinase)

Protein function

Secreted tyrosine-protein kinase that mediates phosphorylation of extracellular proteins and endogenous proteins in the secretory pathway, which is essential for patterning at organogenesis stages. Mediates phosphorylation of MMP1, MMP13, MMP14,

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF12260	PIP49_C	191 → 372	Protein-kinase domain of FAM69	Family

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in platelets. {ECO:0000269|PubMed:25171405}.

Sequence

MRRRRAAVAAGFCASFLLGSVLNVLFAPGSEPPRPGQSPEPSPAPGPGRRGGRGELARQI
RARYEEVQRYSRGGPGPGAGRPERRRLMDLAPGGPGLPRPRPPWARPLSDGAPGWPPAPG
PGSPGPGPRLGCAALRNVSGAQYMGSGYTKAVYRVRLPGGAAVALKAVDFSGHDLGSCVR
EFGVRRGCYRLAAHKLLKEMVLLERLRHPNVLQLYGYCYQDSEDIPDTLTTITELGAPVE
MIQLLQTSWEDRFRICLSLGRLLHHLAHSPLGSVTLLDFRPRQFVLVDGELKVTDLDDAR
VEETPCAGSTDCILEFPARNFTLPCSAQGWCEGMNEKRNLYNAYRFFFTYLLPHSAPPSL
RPLLDSIVNATGELAWGVDETLAQLEKVLHLYRSGQYLQNSTASSSTEYQCIPDSTIPQE
DYRCWPSYHHGSCLLSVFNLAEAVDVCESHAQCRAFVVTNQTTWTGRQLVFFKTGWSQVV
PDPNKTTYVKASG

Sequence length

493

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Rhizomelic limb shortening with dysmorphic features	Likely pathogenic; Pathogenic	rs369267445, rs1158542233, rs2465741582, rs1667907522, rs2465376540, rs2465740345, rs763243200, rs761532715	RCV001813900 RCV003224597 RCV003224624 RCV003224625 RCV002310610 RCV002468684 RCV001027739 RCV001027738 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Abnormality of the skeletal system	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOSPADIAS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PKDCC-related disorder	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Skeletal dysplasia	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (7)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Asthma	Asthma	BEFREE	24407380		★★★★★ ★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	32841424	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood asthma	Asthma	BEFREE	24407380		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	19097194, 19465597, 23559552, 23792766, 25171405		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	Pubtator	27591737	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple congenital anomalies	Multiple Congenital Anomalies	CLINVAR_DG	19097194, 19465597, 23559552, 23792766, 25171405		★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	28508933		★★★★★ ★☆☆☆☆ Found in Text Mining only

PKDCC (protein kinase domain containing, cytoplasmic)