DIPK1C

Summary

DIPK1C (divergent protein kinase domain 1C, HGNC:31729) is a protein-coding gene on chromosome 18q22.3, encoding Divergent protein kinase domain 1C (Q0P6D2).

This gene encodes a member of the FAM69 family of cysteine-rich type II transmembrane proteins. These proteins localize to the endoplasmic reticulum but their specific functions are unknown.

Source: NCBI Gene 125704 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 106 total
• MANE Select transcript: NM_001044369

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31729
Approved symbol	DIPK1C
Name	divergent protein kinase domain 1C
Location	18q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187773
Ensembl biotype	protein_coding
OMIM	614544
Entrez	125704

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000343998, ENST00000400291

RefSeq mRNA: 1 — MANE Select: NM_001044369 NM_001044369

CCDS: CCDS42445

Canonical transcript exons

ENST00000343998 — 4 exons

Exon	Start	End
ENSE00001865627	74434775	74436719
ENSE00002206522	74457062	74457308
ENSE00002306371	74446606	74447283
ENSE00003562121	74441952	74442116

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 90.71.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4000 / max 54.2742, expressed in 151 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
172429	0.4000	151

Top tissues by expression

239 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	90.71	gold quality
putamen	UBERON:0001874	89.20	gold quality
endothelial cell	CL:0000115	87.92	gold quality
caudate nucleus	UBERON:0001873	86.94	gold quality
medial globus pallidus	UBERON:0002477	85.95	gold quality
amygdala	UBERON:0001876	85.90	gold quality
apex of heart	UBERON:0002098	85.72	gold quality
ganglionic eminence	UBERON:0004023	85.67	gold quality
substantia nigra	UBERON:0002038	84.29	gold quality
nucleus accumbens	UBERON:0001882	84.03	gold quality
hypothalamus	UBERON:0001898	83.97	gold quality
globus pallidus	UBERON:0001875	83.40	gold quality
tibia	UBERON:0000979	83.03	gold quality
midbrain	UBERON:0001891	82.95	gold quality
Ammon’s horn	UBERON:0001954	81.11	gold quality
right frontal lobe	UBERON:0002810	80.79	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.67	gold quality
anterior cingulate cortex	UBERON:0009835	79.96	gold quality
temporal lobe	UBERON:0001871	79.89	gold quality
prefrontal cortex	UBERON:0000451	79.59	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	78.81	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.50	gold quality
frontal cortex	UBERON:0001870	78.11	gold quality
cerebral cortex	UBERON:0000956	77.97	gold quality
neocortex	UBERON:0001950	77.87	gold quality
spinal cord	UBERON:0002240	77.65	gold quality
heart left ventricle	UBERON:0002084	76.79	gold quality
forebrain	UBERON:0001890	76.77	gold quality
cardiac ventricle	UBERON:0002082	76.42	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting DIPK1C, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-370-5P	99.78	66.81	706
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-8064	99.45	66.92	875
HSA-MIR-377-3P	99.37	70.18	1905
HSA-MIR-603	98.58	68.28	1603
HSA-MIR-216B-3P	98.55	67.19	1223
HSA-MIR-1914-5P	97.83	66.21	807
HSA-MIR-6793-3P	97.66	65.78	1084
HSA-MIR-342-3P	96.44	67.48	1344
HSA-MIR-6806-5P	96.37	68.74	587
HSA-MIR-549A-5P	96.35	68.08	587

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	dipk1c	ENSDARG00000105040
mus_musculus	Dipk1c	ENSMUSG00000047992
rattus_norvegicus	Dipk1c	ENSRNOG00000015448
drosophila_melanogaster	aln	FBGN0035179
caenorhabditis_elegans	C53D5.1	WBGENE00016902

Paralogs (2): DIPK1A (ENSG00000154511), DIPK1B (ENSG00000165716)

Protein

Protein identifiers

Divergent protein kinase domain 1C — Q0P6D2 (reviewed: Q0P6D2)

Alternative names: Protein FAM69C

All UniProt accessions (1): Q0P6D2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Endoplasmic reticulum membrane.

Post-translational modifications. Among the many cysteines in the lumenal domain, most are probably involved in disulfide bonds.

Similarity. Belongs to the DIPK family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q0P6D2-1	1	yes
Q0P6D2-2	2

RefSeq proteins (1): NP_001037834* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011009	Kinase-like_dom_sf	Homologous_superfamily
IPR022049	FAM69_kinase_dom	Domain
IPR029244	FAM69_N	Domain

Pfam: PF12260, PF14875

UniProt features (6 total): topological domain 2, chain 1, transmembrane region 1, short sequence motif 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q0P6D2-F1	87.13	0.67

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): chr18q22, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, MEISSNER_NPC_HCP_WITH_H3K4ME2, ZWANG_DOWN_BY_2ND_EGF_PULSE, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, MIR466, MIR4789_3P, MIR4643, MIR216B_3P, MIR8064, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_1H_UP, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_2H_UP, GAUTAM_EYE_CORNEA_MELANOCYTES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

368 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DIPK1C	DIPK2B	Q9H7Y0	724
DIPK1C	A0A2Q2T6B6	A0A2Q2T6B6	485
DIPK1C	CHST10	O43529	472
DIPK1C	KLHL30	Q0D2K2	465
DIPK1C	TRMU	O75648	435
DIPK1C	ZNF286A	Q9HBT8	430
DIPK1C	TBC1D8	O95759	408
DIPK1C	C4orf17	Q53FE4	397
DIPK1C	DIPK2A	Q8NDZ4	395
DIPK1C	TCP11L2	Q8N4U5	390
DIPK1C	LONRF2	Q1L5Z9	388
DIPK1C	IRX4	P78413	377
DIPK1C	FAM241A	Q8N8J7	376
DIPK1C	MAL2	Q969L2	371
DIPK1C	CADM2	Q8N3J6	370

IntAct

1 interactions, top by confidence:

BioGRID (4): NSDHL (Proximity Label-MS), CACYBP (Cross-Linking-MS (XL-MS)), FAM69C (Cross-Linking-MS (XL-MS)), FAM69C (Affinity Capture-RNA)

ESM2 similar proteins: A0PJZ3, O35764, O75718, O95390, O95502, P07949, P08571, Q0P6D2, Q32P28, Q3V1T4, Q3V5L5, Q495W5, Q496Z2, Q4KLM6, Q5MJS3, Q5ZEQ8, Q64375, Q6JHU7, Q6JHU8, Q6PVW7, Q810K9, Q86VZ4, Q8BH02, Q8BQT2, Q8CB67, Q8CG64, Q8CG71, Q8CID3, Q8IVL5, Q8IXL6, Q8K1S6, Q8K2B0, Q8TEQ8, Q8WWL2, Q90830, Q92184, Q92791, Q96MK3, Q96NZ8, Q99J85

Diamond homologs: Q0P6D2, Q8BQT2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

106 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	94
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

760 predictions. Top by Δscore:

Variant	Effect	Δscore
18:74436719:CCTG:C	acceptor_loss	1.0000
18:74436721:T:G	acceptor_loss	1.0000
18:74446604:A:AC	donor_gain	1.0000
18:74446605:C:CC	donor_gain	1.0000
18:74457057:CCTA:C	donor_loss	1.0000
18:74457058:CTA:C	donor_loss	1.0000
18:74457059:TA:T	donor_loss	1.0000
18:74457060:A:AC	donor_gain	1.0000
18:74457061:C:CC	donor_gain	1.0000
18:74457061:C:CT	donor_loss	1.0000
18:74436716:TGAC:T	acceptor_gain	0.9900
18:74436720:C:CC	acceptor_gain	0.9900
18:74441946:TCATA:T	donor_loss	0.9900
18:74441947:CATAC:C	donor_loss	0.9900
18:74441949:TACC:T	donor_loss	0.9900
18:74441950:ACC:A	donor_loss	0.9900
18:74441951:C:CG	donor_loss	0.9900
18:74442113:CCAC:C	acceptor_gain	0.9900
18:74442114:CACC:C	acceptor_gain	0.9900
18:74442115:ACCT:A	acceptor_loss	0.9900
18:74442117:C:CA	acceptor_loss	0.9900
18:74442118:T:A	acceptor_loss	0.9900
18:74442119:G:C	acceptor_loss	0.9900
18:74447281:GCAC:G	acceptor_loss	0.9900
18:74447282:CA:C	acceptor_gain	0.9900
18:74447284:C:CC	acceptor_gain	0.9900
18:74447285:T:A	acceptor_loss	0.9900
18:74457061:CCAG:C	donor_gain	0.9900
18:74442114:CAC:C	acceptor_gain	0.9800
18:74445822:T:TA	donor_gain	0.9800

AlphaMissense

2739 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:74441983:C:G	C337S	0.999
18:74441984:A:T	C337S	0.999
18:74442004:C:G	C330S	0.999
18:74442005:A:T	C330S	0.999
18:74442015:A:C	C326W	0.999
18:74442031:C:G	C321S	0.999
18:74442032:A:T	C321S	0.999
18:74442049:C:G	C315S	0.999
18:74442050:A:T	C315S	0.999
18:74446649:C:G	C278S	0.999
18:74446649:C:T	C278Y	0.999
18:74446650:A:T	C278S	0.999
18:74442016:C:G	C326S	0.998
18:74442016:C:T	C326Y	0.998
18:74442017:A:G	C326R	0.998
18:74442017:A:T	C326S	0.998
18:74442030:G:C	C321W	0.998
18:74442031:C:A	C321F	0.998
18:74442031:C:T	C321Y	0.998
18:74442048:G:C	C315W	0.998
18:74442049:C:T	C315Y	0.998
18:74446628:A:C	F285C	0.998
18:74446628:A:G	F285S	0.998
18:74446649:C:A	C278F	0.998
18:74446650:A:G	C278R	0.998
18:74436712:C:T	C350Y	0.997
18:74442016:C:A	C326F	0.997
18:74442049:C:A	C315F	0.997
18:74446648:G:C	C278W	0.997
18:74447134:C:A	K116N	0.997

dbSNP variants (sampled 300 via entrez): RS1000138632 (18:74454623 T>C), RS1000188925 (18:74461720 CT>C), RS1000382808 (18:74456124 A>AT), RS1000480262 (18:74435127 A>G), RS1000520901 (18:74457462 C>A,T), RS1000545705 (18:74464007 T>C), RS1000715360 (18:74457186 A>T), RS1000727515 (18:74461331 C>T), RS1000747033 (18:74457331 C>G,T), RS1000781022 (18:74465125 G>A,T), RS1000981022 (18:74457777 A>G), RS1000990079 (18:74439501 G>A,T), RS1001010758 (18:74441717 C>T), RS1001047103 (18:74439334 G>C,T), RS1001360374 (18:74462091 A>G)

Disease associations

OMIM: gene MIM:614544 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004886_20	Alcohol consumption	2.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects cotreatment	5
methylmercuric chloride	decreases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
entinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
trichostatin A	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
aflatoxin B2	increases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.