DIPK1B

Summary

DIPK1B (divergent protein kinase domain 1B, HGNC:28290) is a protein-coding gene on chromosome 9q34.3, encoding Divergent protein kinase domain 1B (Q5VUD6).

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 138311 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 123 total
• MANE Select transcript: NM_152421

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28290
Approved symbol	DIPK1B
Name	divergent protein kinase domain 1B
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC20262, C9orf136
Ensembl gene	ENSG00000165716
Ensembl biotype	protein_coding
OMIM	614543
Entrez	138311

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000371691, ENST00000371692, ENST00000931510, ENST00000931511, ENST00000931512, ENST00000931513, ENST00000942171

RefSeq mRNA: 1 — MANE Select: NM_152421 NM_152421

CCDS: CCDS7004

Canonical transcript exons

ENST00000371692 — 5 exons

Exon	Start	End
ENSE00001095805	136722125	136722301
ENSE00001195392	136721921	136722028
ENSE00001215423	136717577	136717711
ENSE00001455872	136712572	136712728
ENSE00003843365	136722962	136724742

Expression profiles

Bgee: expression breadth ubiquitous, 222 present calls, max score 94.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.6917 / max 215.4254, expressed in 942 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99535	5.6197	835
99534	2.0719	698

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lateral nuclear group of thalamus	UBERON:0002736	94.74	gold quality
tendon of biceps brachii	UBERON:0008188	92.63	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.46	gold quality
cerebellar hemisphere	UBERON:0002245	90.95	gold quality
cerebellar cortex	UBERON:0002129	90.89	gold quality
cerebellum	UBERON:0002037	90.36	gold quality
apex of heart	UBERON:0002098	90.22	gold quality
endothelial cell	CL:0000115	89.47	gold quality
right frontal lobe	UBERON:0002810	89.33	gold quality
right atrium auricular region	UBERON:0006631	88.95	gold quality
middle temporal gyrus	UBERON:0002771	88.81	gold quality
cardiac atrium	UBERON:0002081	88.74	gold quality
anterior cingulate cortex	UBERON:0009835	88.65	gold quality
cortical plate	UBERON:0005343	88.60	gold quality
Brodmann (1909) area 9	UBERON:0013540	88.56	gold quality
hypothalamus	UBERON:0001898	88.51	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.13	gold quality
right uterine tube	UBERON:0001302	87.84	gold quality
substantia nigra pars compacta	UBERON:0001965	87.77	gold quality
ganglionic eminence	UBERON:0004023	87.74	gold quality
substantia nigra pars reticulata	UBERON:0001966	87.49	gold quality
primary visual cortex	UBERON:0002436	87.36	gold quality
amygdala	UBERON:0001876	87.19	gold quality
putamen	UBERON:0001874	87.02	gold quality
neocortex	UBERON:0001950	87.01	gold quality
nucleus accumbens	UBERON:0001882	86.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.76	gold quality
frontal cortex	UBERON:0001870	86.59	gold quality
brain	UBERON:0000955	86.53	gold quality
cerebral cortex	UBERON:0000956	86.48	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-8207	yes	587.74
E-MTAB-6701	yes	11.77
E-ANND-3	yes	8.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting DIPK1B, 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-6867-5P	100.00	82.21	3464
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-943	97.81	64.42	694
HSA-MIR-5571-3P	97.80	66.07	640
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-6779-3P	97.51	65.82	789
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-1287-5P	96.80	65.30	743
HSA-MIR-342-3P	96.44	67.48	1344
HSA-MIR-7976	95.75	65.67	1186

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	dipk1b	ENSDARG00000117093
mus_musculus	Dipk1b	ENSMUSG00000036186
rattus_norvegicus	Dipk1b	ENSRNOG00000004532
drosophila_melanogaster	aln	FBGN0035179
caenorhabditis_elegans	C53D5.1	WBGENE00016902

Paralogs (2): DIPK1A (ENSG00000154511), DIPK1C (ENSG00000187773)

Protein

Protein identifiers

Divergent protein kinase domain 1B — Q5VUD6 (reviewed: Q5VUD6)

Alternative names: Protein FAM69B

All UniProt accessions (1): Q5VUD6

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?
Q5VUD6-1	1	yes
Q5VUD6-2	2

RefSeq proteins (1): NP_689634* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022049	FAM69_kinase_dom	Domain
IPR029244	FAM69_N	Domain

Pfam: PF12260, PF14875

UniProt features (10 total): topological domain 2, disulfide bond 2, chain 1, transmembrane region 1, short sequence motif 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VUD6-F1	83.25	0.54

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (2): 57–94, 62–117

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, TGACCTY_ERR1_Q2, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, CUI_TCF21_TARGETS_2_UP, TGACCTTG_SF1_Q6, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, KIM_MYCN_AMPLIFICATION_TARGETS_UP, MEISSNER_NPC_HCP_WITH_H3K4ME2, MARTENS_TRETINOIN_RESPONSE_DN, chr9q34, F10_TARGET_GENES, PBXIP1_TARGET_GENES, ZNF7_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

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
binding	1
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

222 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DIPK1B	DIPK2B	Q9H7Y0	572
DIPK1B	SNURF	Q9Y675	370
DIPK1B	KCTD20	Q7Z5Y7	367
DIPK1B	KLHL35	Q6PF15	359
DIPK1B	WASHC2C	Q9Y4E1	324
DIPK1B	N4BP2L2	Q92802	322
DIPK1B	ZNF488	Q96MN9	322
DIPK1B	RUNDC3B	Q96NL0	321
DIPK1B	RUNDC3A	Q59EK9	321
DIPK1B	RPP40	O75818	313
DIPK1B	IHO1	Q8IYA8	311
DIPK1B	RPP38	P78345	310
DIPK1B	CELF5	Q8N6W0	305
DIPK1B	DIPK2A	Q8NDZ4	297
DIPK1B	DNAAF9	Q5TEA3	296
DIPK1B	PKDCC	Q504Y2	296

IntAct

25 interactions, top by confidence:

A	B	Type	Score
SAT1	DIPK1B	psi-mi:“MI:0915”(physical association)	0.720
SLC39A5	FAM171A2	psi-mi:“MI:0914”(association)	0.640
DIPK1A	TMEM259	psi-mi:“MI:0914”(association)	0.530
DIPK1B	VIM	psi-mi:“MI:0915”(physical association)	0.400
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
POMK	ESYT2	psi-mi:“MI:0914”(association)	0.350
LDLRAD1	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
PSCA	METTL15	psi-mi:“MI:0914”(association)	0.350
LRRC52	CANX	psi-mi:“MI:0914”(association)	0.350
SLC30A1	PSMD11	psi-mi:“MI:0914”(association)	0.350
SLC30A10	GOLIM4	psi-mi:“MI:0914”(association)	0.350
SLC39A12	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC39A14	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC39A4	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC39A8	CEBPZOS	psi-mi:“MI:0914”(association)	0.350
SLC3A1	ILVBL	psi-mi:“MI:0914”(association)	0.350
SV2B	C15orf61	psi-mi:“MI:0914”(association)	0.350
DIPK1B	SAT1	psi-mi:“MI:0915”(physical association)	0.000
DIPK1B	RBMS2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (25): FAM69B (Two-hybrid), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), RBMS2 (Two-hybrid), FAM69B (Two-hybrid), FAM69B (Proximity Label-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS), FAM69B (Affinity Capture-MS)

ESM2 similar proteins: A0JPE1, A4D0V7, D3Z2R5, O43916, P97259, Q08834, Q09328, Q1RLQ5, Q3TUA9, Q4V8A9, Q58CX7, Q5F349, Q5FVL3, Q5HZP7, Q5NDE4, Q5NDE5, Q5NDE7, Q5NDE8, Q5R634, Q5R9Q9, Q5RJQ0, Q5T7M9, Q5U3W1, Q5VUD6, Q640M6, Q68CR1, Q6DBY9, Q6DCL6, Q6Q2W4, Q80TS8, Q8C1F4, Q8C3I9, Q8N6G5, Q8NBP0, Q8NHY0, Q8R4G6, Q8R553, Q8WTR4, Q92179, Q95JJ0

Diamond homologs: A0JPE1, Q1RLQ5, Q5FVL3, Q5R634, Q5T7M9, Q5VUD6, Q6DCL6, Q99ML4, Q9D6I7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 31 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Metal ion SLC transporters	5	158.2×	1e-08
SLC-mediated transmembrane transport	6	18.7×	2e-05
Transport of small molecules	7	9.3×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
intracellular monoatomic cation homeostasis	5	224.7×	7e-10
zinc ion transmembrane transport	6	168.5×	9e-11
intracellular zinc ion homeostasis	5	96.3×	6e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	110
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1111 predictions. Top by Δscore:

Variant	Effect	Δscore
9:136712727:AGG:A	donor_loss	1.0000
9:136712729:GTA:G	donor_loss	1.0000
9:136712730:T:G	donor_loss	1.0000
9:136717712:G:GG	donor_gain	1.0000
9:136722297:TCAAG:T	donor_loss	1.0000
9:136722298:CAAGG:C	donor_loss	1.0000
9:136722299:AAGG:A	donor_loss	1.0000
9:136722300:AGG:A	donor_loss	1.0000
9:136722302:G:GA	donor_loss	1.0000
9:136722946:T:TA	acceptor_gain	1.0000
9:136722947:G:A	acceptor_gain	1.0000
9:136722953:A:AG	acceptor_gain	1.0000
9:136722956:C:G	acceptor_gain	1.0000
9:136712725:GCAG:G	donor_gain	0.9900
9:136712729:G:GG	donor_gain	0.9900
9:136717572:CACA:C	acceptor_loss	0.9900
9:136717574:CA:C	acceptor_loss	0.9900
9:136717575:A:AC	acceptor_loss	0.9900
9:136717575:A:AG	acceptor_gain	0.9900
9:136717575:AG:A	acceptor_gain	0.9900
9:136717576:G:GG	acceptor_gain	0.9900
9:136717576:GG:G	acceptor_gain	0.9900
9:136717576:GGGCC:G	acceptor_gain	0.9900
9:136717708:CATTG:C	donor_loss	0.9900
9:136717710:TT:T	donor_gain	0.9900
9:136717712:GTAA:G	donor_loss	0.9900
9:136717713:T:TC	donor_loss	0.9900
9:136717714:A:AG	donor_loss	0.9900
9:136721919:A:AG	acceptor_gain	0.9900
9:136721920:G:GG	acceptor_gain	0.9900

AlphaMissense

2751 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:136723282:G:C	W268C	0.998
9:136723282:G:T	W268C	0.998
9:136723547:T:A	C357S	0.996
9:136723548:G:C	C357S	0.996
9:136723364:T:A	C296S	0.995
9:136723365:G:C	C296S	0.995
9:136723496:T:A	C340S	0.995
9:136723497:G:C	C340S	0.995
9:136723058:G:C	A194P	0.994
9:136723152:G:A	C225Y	0.994
9:136723365:G:A	C296Y	0.994
9:136723587:G:A	C370Y	0.994
9:136723744:G:C	W422C	0.994
9:136723744:G:T	W422C	0.994
9:136723153:T:G	C225W	0.993
9:136723497:G:A	C340Y	0.993
9:136723498:C:G	C340W	0.993
9:136723665:G:A	C396Y	0.993
9:136723666:T:G	C396W	0.993
9:136723366:T:G	C296W	0.992
9:136723478:T:A	C334S	0.992
9:136723479:G:C	C334S	0.992
9:136723728:T:C	L417P	0.992
9:136721960:T:A	C80S	0.991
9:136721961:G:A	C80Y	0.991
9:136721961:G:C	C80S	0.991
9:136721962:C:G	C80W	0.991
9:136723072:G:C	W198C	0.991
9:136723072:G:T	W198C	0.991
9:136723151:T:A	C225S	0.991

dbSNP variants (sampled 300 via entrez): RS1000082088 (9:136724284 C>G,T), RS1000134421 (9:136723991 G>GT), RS1000148518 (9:136719985 G>A), RS1000375420 (9:136721406 A>G,T), RS1000381046 (9:136720515 C>A), RS1000519264 (9:136717156 G>T), RS1000641402 (9:136712091 C>A), RS1001108664 (9:136711835 G>A,C,T), RS1001313255 (9:136723944 G>A), RS1001552213 (9:136721679 G>A), RS1001665801 (9:136719940 G>A,T), RS1001812388 (9:136713096 G>A), RS1002305670 (9:136713356 C>A,T), RS1002334769 (9:136715986 C>T), RS1002393650 (9:136715809 C>T)

Disease associations

OMIM: gene MIM:614543 | 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
GCST90000025_388	Appendicular lean mass	3.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tetrachlorodibenzodioxin	affects expression, increases expression	3
Benzo(a)pyrene	affects methylation, decreases expression	2
bisphenol F	affects cotreatment, increases methylation	1
propionaldehyde	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
aflatoxin B2	decreases methylation	1
pentanal	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Diazinon	increases methylation	1
Doxorubicin	affects expression	1
Methotrexate	increases expression	1
Nickel	decreases expression	1
Pesticides	affects methylation	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	decreases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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