DCP1B

Summary

DCP1B (decapping mRNA 1B, HGNC:24451) is a protein-coding gene on chromosome 12p13.33, encoding mRNA-decapping enzyme 1B (Q8IZD4). May play a role in the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay.

This gene encodes a member of a family of proteins that function in removing the 5’ cap from mRNAs, which is a step in regulated mRNA decay. This protein localizes to cytoplasmic foci which are the site of mRNA breakdown and turnover. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 196513 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 100 total
• MANE Select transcript: NM_152640

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24451
Approved symbol	DCP1B
Name	decapping mRNA 1B
Location	12p13.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31638
Ensembl gene	ENSG00000151065
Ensembl biotype	protein_coding
OMIM	609843
Entrez	196513

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000280665, ENST00000535873, ENST00000536665, ENST00000537725, ENST00000540622, ENST00000541700, ENST00000543381, ENST00000883049, ENST00000883050, ENST00000883051, ENST00000913950, ENST00000913952, ENST00000971563, ENST00000971564

RefSeq mRNA: 2 — MANE Select: NM_152640 NM_001319292, NM_152640

CCDS: CCDS31727, CCDS81651

Canonical transcript exons

ENST00000280665 — 9 exons

Exon	Start	End
ENSE00001159495	2004282	2004457
ENSE00001159501	1946053	1946286
ENSE00003529209	1965558	1965693
ENSE00003541255	1967844	1967910
ENSE00003559353	1955432	1955560
ENSE00003567220	1949086	1949334
ENSE00003583991	1993264	1993391
ENSE00003598894	1952416	1953288
ENSE00003662629	1997935	1997975

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 89.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1756 / max 47.4273, expressed in 1642 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128952	5.1756	1642

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
muscle layer of sigmoid colon	UBERON:0035805	89.64	gold quality
smooth muscle tissue	UBERON:0001135	89.36	gold quality
body of uterus	UBERON:0009853	89.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.65	gold quality
myometrium	UBERON:0001296	88.22	gold quality
right adrenal gland	UBERON:0001233	87.55	gold quality
right adrenal gland cortex	UBERON:0035827	87.26	gold quality
popliteal artery	UBERON:0002250	87.23	gold quality
tibial artery	UBERON:0007610	87.20	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.71	gold quality
lower esophagus	UBERON:0013473	86.68	gold quality
left adrenal gland	UBERON:0001234	86.42	gold quality
urinary bladder	UBERON:0001255	86.14	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	86.07	gold quality
left testis	UBERON:0004533	85.97	gold quality
adrenal gland	UBERON:0002369	85.93	gold quality
left adrenal gland cortex	UBERON:0035825	85.84	gold quality
testis	UBERON:0000473	85.75	gold quality
right testis	UBERON:0004534	85.29	gold quality
colon	UBERON:0001155	85.14	gold quality
fallopian tube	UBERON:0003889	85.02	gold quality
right uterine tube	UBERON:0001302	84.99	gold quality
adrenal tissue	UBERON:0018303	84.66	gold quality
endocervix	UBERON:0000458	84.46	gold quality
prostate gland	UBERON:0002367	84.34	gold quality
islet of Langerhans	UBERON:0000006	84.17	gold quality
pituitary gland	UBERON:0000007	84.07	gold quality
right ovary	UBERON:0002118	83.98	gold quality
adenohypophysis	UBERON:0002196	83.84	gold quality
intestine	UBERON:0000160	83.79	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-7	yes	189.60
E-ENAD-21	yes	182.59
E-ANND-3	no	2.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting DCP1B, 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-1252-5P	100.00	69.80	2774
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-496	98.66	69.80	931
HSA-MIR-1910-3P	98.44	67.51	1695
HSA-MIR-6511A-5P	98.13	67.47	1770
HSA-MIR-217-3P	95.67	68.42	1000
HSA-MIR-659-5P	95.36	65.00	300

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	dcp1b	ENSDARG00000045484
mus_musculus	Dcp1b	ENSMUSG00000041477
rattus_norvegicus	Dcp1b	ENSRNOG00000007340
drosophila_melanogaster	DCP1	FBGN0034921
caenorhabditis_elegans		WBGENE00021929

Paralogs (1): DCP1A (ENSG00000272886)

Protein

Protein identifiers

mRNA-decapping enzyme 1B — Q8IZD4 (reviewed: Q8IZD4)

All UniProt accessions (4): Q8IZD4, B4DVJ6, F5GZK9, F5H4R4

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. May remove the 7-methyl guanine cap structure from mRNA molecules, yielding a 5’-phosphorylated mRNA fragment and 7m-GDP.

Subunit / interactions. Interacts with DCP1A. (Microbial infection) Interacts with rotavirus A non-structural protein 2; this interaction probably plays a role in the sequestration of DCP1B in viral factories. Interacts with rotavirus A non-structural protein 5; this interaction probably plays a role in its sequestration in viral factories.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the DCP1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IZD4-1	1	yes
Q8IZD4-2	2

RefSeq proteins (2): NP_001306221, NP_689853* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010334	Dcp1	Family
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR031953	mRNA_decap_C	Domain

Pfam: PF06058, PF16741

Catalyzed reactions (Rhea), 1 shown:

• a 5’-end (N(7)-methyl 5’-triphosphoguanosine)-ribonucleoside in mRNA + H2O = N(7)-methyl-GDP + a 5’-end phospho-ribonucleoside in mRNA + 2 H(+) (RHEA:67484)

UniProt features (24 total): modified residue 8, sequence variant 4, region of interest 3, sequence conflict 3, compositionally biased region 3, initiator methionine 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IZD4-F1	58.19	0.22

Functional residue map

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

Post-translational modifications (8): 191, 275, 336, 392, 448, 511, 2, 147

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-430039	mRNA decay by 5’ to 3’ exoribonuclease

MSigDB gene sets: 138 (showing top): GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_DEADENYLATION_DEPENDENT_DECAY, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_NONSENSE_MEDIATED_DECAY, REACTOME_METABOLISM_OF_RNA, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOMF_MRNA_BINDING, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, GOMF_ENZYME_ACTIVATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY

GO Biological Process (4): nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184), deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290), deadenylation-independent decapping of nuclear-transcribed mRNA (GO:0031087), positive regulation of catalytic activity (GO:0043085)

GO Molecular Function (5): mRNA binding (GO:0003729), enzyme activator activity (GO:0008047), 5’-(N(7)-methylguanosine 5’-triphospho)-[mRNA] hydrolase activity (GO:0140933), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (5): P-body (GO:0000932), nucleus (GO:0005634), cytosol (GO:0005829), membrane (GO:0016020), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Deadenylation-dependent mRNA decay	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
catalytic activity	3
cellular anatomical structure	3
nuclear-transcribed mRNA catabolic process	2
mRNA methylguanosine-cap decapping	2
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	1
nuclear-transcribed mRNA catabolic process, deadenylation-independent decay	1
positive regulation of molecular function	1
regulation of catalytic activity	1
RNA binding	1
enzyme regulator activity	1
molecular function activator activity	1
pyrophosphatase activity	1
binding	1
cytoplasmic ribonucleoprotein granule	1
intracellular membrane-bounded organelle	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1046 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DCP1B	XRN1	Q8IZH2	854
DCP1B	DCP2	Q8IU60	844
DCP1B	EDC3	Q96F86	833
DCP1B	DDX6	P26196	793
DCP1B	EDC4	Q6P2E9	780
DCP1B	UPF1	Q92900	776
DCP1B	ATXN2L	Q8WWM7	608
DCP1B	LSM1	O15116	606
DCP1B	ATXN2	Q99700	570
DCP1B	PATL1	Q86TB9	528
DCP1B	LSM14B	Q9BX40	526
DCP1B	PABPC1	P11940	503
DCP1B	DCPS	Q96C86	490
DCP1B	LSM4	Q9Y4Z0	483
DCP1B	BNIPL	Q7Z465	481

IntAct

142 interactions, top by confidence:

A	B	Type	Score
EDC3	DDX6	psi-mi:“MI:0914”(association)	0.960
DCP1A	DCP2	psi-mi:“MI:0914”(association)	0.950
EDC3	DCP1B	psi-mi:“MI:0915”(physical association)	0.930
DCP1B	EDC3	psi-mi:“MI:0915”(physical association)	0.930
DCP1A	DDX6	psi-mi:“MI:0914”(association)	0.930
DCP1B	DDX6	psi-mi:“MI:0914”(association)	0.890
ATXN2	PABPC1	psi-mi:“MI:0915”(physical association)	0.820
DDX6	EDC4	psi-mi:“MI:0914”(association)	0.820
DCP1A	DCP1B	psi-mi:“MI:0403”(colocalization)	0.760
DCP1A	DCP1B	psi-mi:“MI:0915”(physical association)	0.760
DCP1A	DCP1B	psi-mi:“MI:0914”(association)	0.760
DCP1B	DCP2	psi-mi:“MI:0914”(association)	0.740
DCP1B	BAG4	psi-mi:“MI:0915”(physical association)	0.670
ZNF704	SAP30	psi-mi:“MI:0914”(association)	0.640
EDC3	BAG4	psi-mi:“MI:0914”(association)	0.640
LPXN	PCNT	psi-mi:“MI:0914”(association)	0.640
NBDY	EDC4	psi-mi:“MI:0914”(association)	0.640
CHCHD4	SSNA1	psi-mi:“MI:0914”(association)	0.640
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
ERP44	TGFB1	psi-mi:“MI:0914”(association)	0.640

BioGRID (194): DCP1B (Two-hybrid), DCP1B (Two-hybrid), DCP1B (Two-hybrid), DCP1B (Two-hybrid), DCP1B (Reconstituted Complex), DCP1B (Affinity Capture-MS), DCP1B (Affinity Capture-MS), DCP1B (Affinity Capture-MS), DCP1B (Affinity Capture-MS), DCP1B (Affinity Capture-MS), DCP1B (Affinity Capture-MS), DCP1B (Proximity Label-MS), DCP1B (Proximity Label-MS), DCP1B (Proximity Label-MS), DCP1B (Proximity Label-MS)

ESM2 similar proteins: A0JM64, A4IHD9, B5DF93, D3ZTQ1, E7F1H9, O70305, P70501, Q12872, Q13625, Q2NLB0, Q2T9I5, Q32SG5, Q3TC46, Q3TCX3, Q3USH5, Q498K9, Q566L7, Q5R413, Q5R8Q4, Q5SFM8, Q5T8P6, Q5ZL54, Q62415, Q66IJ0, Q68FI1, Q6DDU9, Q6GP15, Q6NXI6, Q6NZ18, Q6NZN0, Q6PEH8, Q7Z7F0, Q86TB9, Q8BG81, Q8CG79, Q8CGC4, Q8IZD4, Q8K2F8, Q8ND56, Q8R205

Diamond homologs: I3LHS8, Q3SZL6, Q3U564, Q5R413, Q8IZD4, Q91YD3, Q9NPI6, Q9P805, Q9SJF3, Q9N363

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 126 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
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	57.4×	6e-09
Activation of BAD and translocation to mitochondria	6	55.7×	6e-08
mRNA decay by 5’ to 3’ exoribonuclease	6	55.7×	6e-08
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	6	49.1×	1e-07
Activation of BH3-only proteins	6	36.3×	8e-07
RHO GTPases activate PKNs	6	23.2×	9e-06
Intrinsic Pathway for Apoptosis	6	21.4×	1e-05
FOXO-mediated transcription	5	20.5×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	5	21.7×	7e-04
protein targeting	6	20.4×	2e-04
substantia nigra development	5	17.0×	2e-03
intracellular protein localization	7	6.8×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	6
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1736 predictions. Top by Δscore:

Variant	Effect	Δscore
12:1949275:C:CT	acceptor_gain	1.0000
12:1952411:TTTA:T	donor_loss	1.0000
12:1952412:TTACC:T	donor_loss	1.0000
12:1952413:TACC:T	donor_loss	1.0000
12:1955426:CCGTA:C	donor_loss	1.0000
12:1955427:CGTAC:C	donor_loss	1.0000
12:1955429:TAC:T	donor_loss	1.0000
12:1955430:A:AC	donor_gain	1.0000
12:1955430:A:C	donor_loss	1.0000
12:1955431:C:CC	donor_gain	1.0000
12:1955556:TTACA:T	acceptor_gain	1.0000
12:1955557:TACA:T	acceptor_gain	1.0000
12:1955558:ACA:A	acceptor_gain	1.0000
12:1955559:CA:C	acceptor_gain	1.0000
12:1955559:CAC:C	acceptor_gain	1.0000
12:1955560:AC:A	acceptor_loss	1.0000
12:1955561:C:CC	acceptor_gain	1.0000
12:1965553:CTCA:C	donor_loss	1.0000
12:1965554:TCA:T	donor_loss	1.0000
12:1965555:CACC:C	donor_loss	1.0000
12:1965556:A:AC	donor_gain	1.0000
12:1965556:AC:A	donor_gain	1.0000
12:1965557:C:CG	donor_gain	1.0000
12:1965557:CC:C	donor_gain	1.0000
12:1965557:CCT:C	donor_gain	1.0000
12:1965557:CCTT:C	donor_gain	1.0000
12:1965557:CCTTT:C	donor_gain	1.0000
12:1965689:TTAGG:T	acceptor_gain	1.0000
12:1965690:TAGG:T	acceptor_gain	1.0000
12:1965691:AGG:A	acceptor_gain	1.0000

AlphaMissense

4029 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:1967888:A:C	F114L	1.000
12:1967888:A:T	F114L	1.000
12:1967889:A:G	F114S	1.000
12:1967890:A:G	F114L	1.000
12:1967893:A:G	W113R	1.000
12:1967893:A:T	W113R	1.000
12:1967898:C:T	G111E	1.000
12:1993281:A:G	L101P	1.000
12:1993284:A:G	L100P	1.000
12:1993286:G:C	F99L	1.000
12:1993286:G:T	F99L	1.000
12:1993287:A:G	F99S	1.000
12:1993288:A:G	F99L	1.000
12:1993352:C:A	R77S	1.000
12:1993352:C:G	R77S	1.000
12:1993353:C:A	R77M	1.000
12:1993355:A:C	N76K	1.000
12:1993355:A:T	N76K	1.000
12:1993362:A:T	I74N	1.000
12:1993368:A:G	F72S	1.000
12:1997935:C:A	R64M	1.000
12:1997944:A:T	V61D	1.000
12:1997946:A:C	F60L	1.000
12:1997946:A:T	F60L	1.000
12:1997947:A:G	F60S	1.000
12:1997948:A:G	F60L	1.000
12:1997956:C:A	G57V	1.000
12:1997956:C:T	G57E	1.000
12:1997957:C:G	G57R	1.000
12:1997957:C:T	G57R	1.000

dbSNP variants (sampled 300 via entrez): RS1000064599 (12:1997433 T>G), RS1000246888 (12:1990736 A>G), RS1000270285 (12:1941925 G>T), RS1000324735 (12:1978172 C>G,T), RS1000338283 (12:2005880 G>A), RS1000377064 (12:1999596 C>T), RS1000435183 (12:1984554 T>C), RS1000453995 (12:1948362 C>A), RS1000479247 (12:1957949 G>A,T), RS1000495292 (12:1958115 G>A), RS1000562782 (12:2002416 A>T), RS1000652398 (12:1977858 T>A,C), RS1000759162 (12:1970825 G>A,C), RS1000765639 (12:1980275 C>T), RS1000853891 (12:1960149 C>T)

Disease associations

OMIM: gene MIM:609843 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001346_3	Response to gemcitabine in pancreatic cancer	8.000000e-06
GCST001762_877	Obesity-related traits	8.000000e-06
GCST001877_67	Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined)	5.000000e-09
GCST004485_16	Survival in pancreatic cancer	8.000000e-06
GCST008531_1	Grapefruit juice consumption	6.000000e-07
GCST009391_779	Metabolite levels	2.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004627	IGF-1 measurement
EFO:0000638	overall survival
EFO:0010094	grapefruit juice consumption measurement
EFO:0010394	sphingomyelin 18:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs11062040	CACNA1C, DCP1B		0.00	0
rs2041135	CACNA1C, DCP1B		0.00	0

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	4
Valproic Acid	affects expression, decreases expression	3
Formaldehyde	decreases expression, increases expression	2
Aflatoxin B1	affects expression, increases expression	2
GSK-J4	decreases expression	1
FR900359	affects phosphorylation	1
zinc chloride	affects cotreatment, decreases expression	1
sodium arsenite	decreases expression, increases abundance	1
perfluorooctane sulfonic acid	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Cadmium	decreases expression, increases abundance	1
Caffeine	affects phosphorylation	1
Enzyme Inhibitors	increases O-linked glycosylation, decreases activity	1
Ethyl Methanesulfonate	increases expression	1
Clioquinol	affects cotreatment, decreases expression	1
Lead	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Urethane	decreases expression	1
Cadmium Chloride	increases abundance, decreases expression	1
Copper Sulfate	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E0VI	Ubigene Huh-7 DCP1B KO	Cancer cell line	Male

Clinical trials (associated diseases)

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