PKDCC (protein kinase domain containing, cytoplasmic)

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Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 91461
• Gene name: Protein kinase domain containing, cytoplasmic
• Gene symbol: PKDCC
• Synonyms (NCBI Gene): RLSDF, SGK493, Vlk
• Chromosome: 2
• Chromosome location: 2p21

SNPs

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

miRNA 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

Gene ontology (GO) 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

Other IDs

• MIM: 614150
• HGNC: 25123
• e!Ensembl: ENSG00000162878

Protein

• UniProt ID: 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

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
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	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (15)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Abnormality of the skeletal system	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	35589863	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANDROGENETIC ALOPECIA	—	GWAS catalog	30573740	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	36810956	★★☆☆☆ 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	25108383	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	35835914	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	34062886	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CANCER	—	GWAS catalog	34062886	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CARCINOMA	—	GWAS catalog	34062886	★★☆☆☆ 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	34062886	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (7)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
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

Related Genes

DNAH6 1 shared diseaseHypospadias 2 shared evidence sourcesGWAS catalog (Astrocytoma), GWAS catalog (Hypospadias) Related via 1 shared disease including Hypospadias — evidence mostly GWAS catalog.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
DNAH6	1	["Hypospadias"]	0	[]	2	["GWAS catalog (Astrocytoma)","GWAS catalog (Hypospadias)"]

Diseases Linked via Similar Genes

Ciliary dyskinesia Linked via 1 of 1 related geneDNAH6 Focal segmental glomerulosclerosis Linked via 1 of 1 related geneDNAH6 Major depressive disorder Linked via 1 of 1 related geneDNAH6 Male infertility single gene azoospermia Linked via 1 of 1 related geneDNAH6 Premature ovarian failure Linked via 1 of 1 related geneDNAH6

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Ciliary dyskinesia	1	["DNAH6"]
Focal segmental glomerulosclerosis	1	["DNAH6"]
Major depressive disorder	1	["DNAH6"]
Male infertility single gene azoospermia	1	["DNAH6"]
Premature ovarian failure	1	["DNAH6"]