DCP1A

Summary

DCP1A (decapping mRNA 1A, HGNC:18714) is a protein-coding gene on chromosome 3p21.1, encoding mRNA-decapping enzyme 1A (Q9NPI6). Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay.

Decapping is a key step in general and regulated mRNA decay. The protein encoded by this gene is a decapping enzyme. This protein and another decapping enzyme form a decapping complex, which interacts with the nonsense-mediated decay factor hUpf1 and may be recruited to mRNAs containing premature termination codons. This protein also participates in the TGF-beta signaling pathway. Alternative splicing of this gene results in multiple transcript variants.

Source: NCBI Gene 55802 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_018403

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18714
Approved symbol	DCP1A
Name	decapping mRNA 1A
Location	3p21.1
Locus type	gene with protein product
Status	Approved
Aliases	HSA275986, SMIF, SMAD4IP1
Ensembl gene	ENSG00000272886
Ensembl biotype	protein_coding
OMIM	607010
Entrez	55802

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 16 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000294241, ENST00000558034, ENST00000559748, ENST00000560076, ENST00000560624, ENST00000610213, ENST00000863995, ENST00000863996, ENST00000863997, ENST00000863998, ENST00000863999, ENST00000864000, ENST00000918278, ENST00000918279, ENST00000918280, ENST00000918281, ENST00000956912, ENST00000956913

RefSeq mRNA: 5 — MANE Select: NM_018403 NM_001290204, NM_001290205, NM_001290206, NM_001290207, NM_018403

CCDS: CCDS46847, CCDS74946

Canonical transcript exons

ENST00000610213 — 10 exons

Exon	Start	End
ENSE00003586516	53347383	53347543
ENSE00003707796	53290791	53290856
ENSE00003710817	53283429	53287660
ENSE00003726622	53319407	53319473
ENSE00003730542	53292069	53292827
ENSE00003731245	53288065	53288283
ENSE00003734573	53304177	53304290
ENSE00003734899	53342144	53342271
ENSE00003742558	53312241	53312379
ENSE00003749514	53344902	53344942

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 98.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.9627 / max 151.8242, expressed in 1795 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42513	14.7626	1793
42512	0.2001	91

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.14	gold quality
secondary oocyte	CL:0000655	97.14	gold quality
cartilage tissue	UBERON:0002418	91.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.26	gold quality
calcaneal tendon	UBERON:0003701	88.61	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.69	gold quality
sural nerve	UBERON:0015488	86.97	gold quality
tibialis anterior	UBERON:0001385	86.75	silver quality
buccal mucosa cell	CL:0002336	86.69	gold quality
islet of Langerhans	UBERON:0000006	86.41	gold quality
nipple	UBERON:0002030	86.34	gold quality
germinal epithelium of ovary	UBERON:0001304	84.90	gold quality
colonic epithelium	UBERON:0000397	84.74	gold quality
tendon	UBERON:0000043	84.71	gold quality
parietal pleura	UBERON:0002400	84.71	gold quality
bone marrow	UBERON:0002371	84.53	gold quality
parotid gland	UBERON:0001831	84.47	gold quality
left ventricle myocardium	UBERON:0006566	84.39	silver quality
adrenal tissue	UBERON:0018303	84.26	gold quality
tibia	UBERON:0000979	84.24	gold quality
placenta	UBERON:0001987	84.13	gold quality
ileal mucosa	UBERON:0000331	84.11	gold quality
pleura	UBERON:0000977	83.97	gold quality
cerebellar vermis	UBERON:0004720	83.88	gold quality
amniotic fluid	UBERON:0000173	83.80	gold quality
mucosa of urinary bladder	UBERON:0001259	83.67	gold quality
bone marrow cell	CL:0002092	83.65	gold quality
ovary	UBERON:0000992	83.57	gold quality
thymus	UBERON:0002370	83.56	gold quality
Brodmann (1909) area 23	UBERON:0013554	83.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

166 targeting DCP1A, 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-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-144-3P	99.94	73.98	2698

Literature-anchored findings (GeneRIF, showing 19)

• Overexpression of wild-type SMIF enhanced expression of TGFbeta/BMP regulated genes, whereas a dominant-negative SMIF mutant suppressed expression. (PMID:11836524)
• These data suggest that a human decapping complex containing decapping enzymes hDcp1a and hDcp2 may be recruited to mRNAs containing premature termination codons by the hUpf proteins. (PMID:12417715)
• Data show the presence of P-body-like foci in mouse oocytes, as revealed by the presence of Dcp1a and the colocalization of RNA-associated protein 55 (RAP55) and the DEAD box RNA helicase Rck/p54. (PMID:19812249)
• Reveal DCP1a as a multifunctional regulator of mRNA expression and suggest a role for JNK kinase phosphorylation in controlling the subcellular localization of DCP1a in response to stress or inflammatory stimuli. (PMID:21859862)
• PNRC2 acts in synergy with Dcp1a to stimulate the decapping activity of Dcp2 by bridging the interaction between Dcp1a and Dcp2. (PMID:23085078)
• Malin regulates the recruitment of mRNA-decapping enzyme 1A (Dcp1a) to processing bodies. (PMID:23131811)
• hDcp1a has a role in control of processing body dynamics during the cell cycle via phosphorylation (PMID:23300942)
• The data indicates that DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5’-to-3’ mRNA degradation by XRN1 in human cells. (PMID:24510189)
• Phosphorylation at serine 315, serine 319, and threonine 321 of DCP1A modulates IL-8 expression during respiratory syncytial virus infection. (PMID:25796077)
• The assembly of EDC4 and Dcp1a into processing bodies is critical for the translational regulation of IL-6. (PMID:25970328)
• The E3 ligase TRAF6 binds to DCP1a and indirectly regulates DCP1a phosphorylation, expression of decapping factors, and gene-specific mRNA decay. (PMID:27315556)
• DCP1A rs11551405 may have a prognostic effect on survival of CM patients. (PMID:27578485)
• The results suggest that overexpressed Dcp1a and GW182 can form different cytoplasmic aggregates and play distinct biological roles in the miRNA pathway. (PMID:28488892)
• Overexpression of DCP1A is associated with malignant melanoma. (PMID:29076924)
• Results suggest a molecular mechanism of long non-coding RNA (MALAT1)-miR203-mRNA-decapping enzymes 1a (DCP1A) axis which is involved with the development and contributes to the malignancy of colorectal cancers. (PMID:29964337)
• Human MARF1 is an endoribonuclease that interacts with the DCP1:DCP2 decapping complex and degrades target mRNAs. (PMID:30364987)
• Expression of DCP1a in gastric cancer and its biological function and mechanism in chemotherapy resistance in gastric cancer cells. (PMID:32646734)
• Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover. (PMID:32807903)
• DCP1A is an unfavorable prognostic-related enhancer RNA in hepatocellular carcinoma. (PMID:34609335)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	dcp1a	ENSDARG00000100136
mus_musculus	Dcp1a	ENSMUSG00000021962
rattus_norvegicus	Dcp1a	ENSRNOG00000016015
drosophila_melanogaster	DCP1	FBGN0034921
caenorhabditis_elegans		WBGENE00021929

Paralogs (1): DCP1B (ENSG00000151065)

Protein

Protein identifiers

mRNA-decapping enzyme 1A — Q9NPI6 (reviewed: Q9NPI6)

Alternative names: Smad4-interacting transcriptional co-activator, Transcription factor SMIF

All UniProt accessions (4): A0A087WT55, A0A087WVE6, A0A087WXD0, Q9NPI6

UniProt curated annotations — full annotation on UniProt →

Function. Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5’-phosphorylated mRNA fragment and 7m-GDP. Contributes to the transactivation of target genes after stimulation by TGFB1. Essential for embryonic development.

Subunit / interactions. (Microbial infection) Interacts with rotavirus A non-structural protein 2; this interaction probably plays a role in the sequestration of DCP1A in viral factories. Interacts with rotavirus A non-structural protein 5; this interaction probably plays a role in its sequestration in viral factories. Forms a complex with EDC3, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with EDC3. Part of a cytoplasmic complex containing proteins involved in mRNA decay, including XRN1 and LSM1. Interacts with DCP1B. Interacts with DCP2. Interacts with DDX17 in an RNA-independent manner. Interacts with PNRC2. Interacts with SMAD4. Interacts with UPF1. Interacts with ZC3HAV1. Interacts with ZFP36L1. Interacts with NBDY. Interacts with DHX34; the interaction is RNA-independent.

Subcellular location. Cytoplasm. P-body. Nucleus.

Tissue specificity. Detected in heart, brain, placenta, lung, skeletal muscle, liver, kidney and pancreas.

Similarity. Belongs to the DCP1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NPI6-1	1	yes
Q9NPI6-2	2

RefSeq proteins (5): NP_001277133, NP_001277134, NP_001277135, NP_001277136, NP_060873* (*=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 (40 total): modified residue 17, strand 7, helix 4, region of interest 3, compositionally biased region 3, mutagenesis site 2, chain 1, splice variant 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
2WX3	X-RAY DIFFRACTION	2.31
4B6H	X-RAY DIFFRACTION	2.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NPI6-F1	59.22	0.28

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 (17): 180, 315, 319, 334, 348, 353, 376, 401, 422, 522, 523, 525, 528, 531, 62, 142, 179

Mutagenesis-validated functional residues (2):

Position	Phenotype
20	lowers decapping activity.
59	lowers decapping activity.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-430039	mRNA decay by 5’ to 3’ exoribonuclease
R-HSA-450385	Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-HSA-450513	Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

MSigDB gene sets: 246 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, CACCAGC_MIR138, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, FOSTER_TOLERANT_MACROPHAGE_UP, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_DEADENYLATION_DEPENDENT_DECAY, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOCC_NEURON_PROJECTION

GO Biological Process (6): 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), mRNA methylguanosine-cap decapping (GO:0110156), protein localization to cytoplasmic stress granule (GO:1903608), positive regulation of catalytic activity (GO:0043085)

GO Molecular Function (7): mRNA binding (GO:0003729), enzyme activator activity (GO:0008047), kinesin binding (GO:0019894), identical protein binding (GO:0042802), 5’-(N(7)-methylguanosine 5’-triphospho)-[mRNA] hydrolase activity (GO:0140933), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (7): P-body (GO:0000932), nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), dendrite (GO:0030425), cytoplasmic ribonucleoprotein granule (GO:0036464)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Regulation of mRNA stability by proteins that bind AU-rich elements	2
Deadenylation-dependent mRNA decay	1
Nonsense-Mediated Decay (NMD)	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
cytoplasm	2
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	1
nuclear-transcribed mRNA catabolic process, deadenylation-independent decay	1
mRNA metabolic process	1
RNA decapping	1
protein localization to organelle	1
positive regulation of molecular function	1
regulation of catalytic activity	1
RNA binding	1
enzyme regulator activity	1
molecular function activator activity	1
cytoskeletal protein binding	1
protein binding	1
pyrophosphatase activity	1
binding	1
cytoplasmic ribonucleoprotein granule	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
neuron projection	1
dendritic tree	1
ribonucleoprotein granule	1

Protein interactions and networks

STRING

1736 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DCP1A	EDC4	Q6P2E9	999
DCP1A	DCP2	Q8IU60	999
DCP1A	DDX6	P26196	992
DCP1A	EDC3	Q96F86	988
DCP1A	XRN1	Q8IZH2	984
DCP1A	PNRC2	Q9NPJ4	980
DCP1A	UPF1	Q92900	949
DCP1A	TNRC6A	Q8NDV7	942
DCP1A	AGO2	Q9UKV8	861
DCP1A	LSM1	O15116	839
DCP1A	MEX3A	A1L020	830
DCP1A	LSM14A	Q8ND56	814
DCP1A	MEX3B	Q6ZN04	808
DCP1A	AGO1	Q9UL18	807
DCP1A	DICER1	Q9UPY3	801

IntAct

236 interactions, top by confidence:

A	B	Type	Score
EDC3	DDX6	psi-mi:“MI:0914”(association)	0.960
DCP1A	EDC3	psi-mi:“MI:0403”(colocalization)	0.950
DCP1A	DCP2	psi-mi:“MI:0914”(association)	0.950
DCP2	DCP1A	psi-mi:“MI:0915”(physical association)	0.950
DCP1A	DCP2	psi-mi:“MI:0403”(colocalization)	0.950
EDC3	DCP1A	psi-mi:“MI:0915”(physical association)	0.950
DCP1A	EDC3	psi-mi:“MI:0915”(physical association)	0.950
DCP1A	DCP2	psi-mi:“MI:0915”(physical association)	0.950
DCP2	DCP1A	psi-mi:“MI:0914”(association)	0.950
PNRC2	DCP1A	psi-mi:“MI:0915”(physical association)	0.940
DCP1A	PNRC2	psi-mi:“MI:0915”(physical association)	0.940
PNRC2	DCP1A	psi-mi:“MI:0403”(colocalization)	0.940
DDX6	DCP1A	psi-mi:“MI:0403”(colocalization)	0.930
DCP1A	DDX6	psi-mi:“MI:0915”(physical association)	0.930
DDX6	DCP1A	psi-mi:“MI:0915”(physical association)	0.930

BioGRID (313): DCP1A (Two-hybrid), DCP1A (Two-hybrid), RITA1 (Two-hybrid), DCP1A (Reconstituted Complex), DCP1A (Two-hybrid), DCP1A (Two-hybrid), DCP1A (Reconstituted Complex), DCP1A (Affinity Capture-MS), DCP1A (Affinity Capture-MS), DCP1A (Affinity Capture-MS), DCP1A (Affinity Capture-MS), DCP1A (Affinity Capture-MS), DCP1A (Proximity Label-MS), DCP1A (Affinity Capture-MS), DDX6 (Affinity Capture-MS)

ESM2 similar proteins: A2VE56, A6QPH9, I3LHS8, O08781, O14545, O54836, P0C6S7, Q14CM0, Q3SZY7, Q3U2E2, Q497H0, Q4R3D6, Q4R970, Q58D05, Q5F3F2, Q5FWF5, Q5R7S6, Q5RDJ2, Q5U2M7, Q5VT97, Q66J85, Q68FE8, Q69Z69, Q6DGF4, Q6FIF0, Q6N043, Q6P2K3, Q70EL2, Q7Z6G8, Q8BIZ1, Q8IWR0, Q8K214, Q8K387, Q8N7W2, Q8N9Z9, Q8NA31, Q8ND82, Q8QFX1, Q91YD3, Q96B23

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 108 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	8	60.4×	1e-10
Activation of BAD and translocation to mitochondria	7	59.9×	1e-09
mRNA decay by 5’ to 3’ exoribonuclease	7	59.9×	1e-09
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	52.8×	3e-09
Activation of BH3-only proteins	7	39.0×	3e-08
Intrinsic Pathway for Apoptosis	8	26.3×	4e-08
RHO GTPases activate PKNs	7	24.9×	6e-07
FOXO-mediated transcription	6	22.6×	8e-06

GO biological processes:

GO term	Partners	Fold	FDR
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	7	33.4×	1e-06
protein targeting	6	22.4×	6e-05
intracellular protein localization	8	8.5×	9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	64
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1561 predictions. Top by Δscore:

Variant	Effect	Δscore
3:53288061:ATAC:A	donor_loss	1.0000
3:53288282:AC:A	acceptor_gain	1.0000
3:53288283:CC:C	acceptor_gain	1.0000
3:53290857:C:CC	acceptor_gain	1.0000
3:53290862:A:AC	acceptor_gain	1.0000
3:53290866:T:C	acceptor_gain	1.0000
3:53290866:T:TC	acceptor_gain	1.0000
3:53290868:A:C	acceptor_gain	1.0000
3:53292824:CAGA:C	acceptor_gain	1.0000
3:53292828:C:CC	acceptor_gain	1.0000
3:53312239:AC:A	donor_gain	1.0000
3:53312240:CC:C	donor_gain	1.0000
3:53312240:CCCT:C	donor_gain	1.0000
3:53312249:A:AC	donor_gain	1.0000
3:53312250:C:CC	donor_gain	1.0000
3:53312253:A:AC	donor_gain	1.0000
3:53312253:AT:A	donor_gain	1.0000
3:53312253:ATC:A	donor_gain	1.0000
3:53312254:T:C	donor_gain	1.0000
3:53312254:T:TA	donor_gain	1.0000
3:53312375:CCACA:C	acceptor_gain	1.0000
3:53312376:CACA:C	acceptor_gain	1.0000
3:53312376:CACAC:C	acceptor_gain	1.0000
3:53312378:CA:C	acceptor_gain	1.0000
3:53312380:C:CC	acceptor_gain	1.0000
3:53319472:CA:C	acceptor_gain	1.0000
3:53319472:CACT:C	acceptor_gain	1.0000
3:53319474:C:CC	acceptor_gain	1.0000
3:53319475:T:C	acceptor_gain	1.0000
3:53319475:T:TC	acceptor_gain	1.0000

AlphaMissense

3799 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:53288072:A:G	L554P	1.000
3:53319428:C:G	R117P	1.000
3:53319433:A:C	C115W	1.000
3:53319434:C:T	C115Y	1.000
3:53319451:A:C	F109L	1.000
3:53319451:A:T	F109L	1.000
3:53319452:A:G	F109S	1.000
3:53319453:A:G	F109L	1.000
3:53319456:A:G	W108R	1.000
3:53319456:A:T	W108R	1.000
3:53319458:A:T	I107N	1.000
3:53319460:A:C	S106R	1.000
3:53319460:A:T	S106R	1.000
3:53319462:T:G	S106R	1.000
3:53319467:A:T	I104K	1.000
3:53342154:T:A	R98S	1.000
3:53342154:T:G	R98S	1.000
3:53342159:A:C	Y97D	1.000
3:53342161:A:G	L96P	1.000
3:53342164:A:C	L95R	1.000
3:53342164:A:G	L95P	1.000
3:53342164:A:T	L95H	1.000
3:53342166:A:C	F94L	1.000
3:53342166:A:T	F94L	1.000
3:53342167:A:G	F94S	1.000
3:53342168:A:G	F94L	1.000
3:53342185:A:G	F88S	1.000
3:53342215:A:G	L78P	1.000
3:53342230:A:G	L73P	1.000
3:53342233:C:G	R72P	1.000

dbSNP variants (sampled 300 via entrez): RS1000001319 (3:53296170 C>T), RS1000168137 (3:53331366 A>T), RS1000266445 (3:53317139 A>G), RS1000379307 (3:53323195 T>G), RS1000385577 (3:53322997 T>C), RS1000446587 (3:53329020 T>C), RS1000463086 (3:53311320 G>C), RS1000515854 (3:53345614 G>A), RS1000572865 (3:53346147 T>C), RS1000574290 (3:53306283 C>A,G), RS1000805043 (3:53299901 T>A), RS1000839542 (3:53328628 A>C), RS1000868407 (3:53318408 G>A,C), RS1000890063 (3:53287169 G>A), RS1000975126 (3:53324401 C>G)

Disease associations

OMIM: gene MIM:607010 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST001969_26	Heart rate	7.000000e-06
GCST002542_5	Electrocardiographic traits	4.000000e-07
GCST002752_1	Spontaneous preterm birth (preterm delivery)	5.000000e-06
GCST005951_50	Body mass index	5.000000e-11
GCST006218_14	Erosive tooth wear (severe vs non-severe)	4.000000e-08
GCST006218_15	Erosive tooth wear (severe vs non-severe)	3.000000e-08
GCST010002_424	Refractive error	9.000000e-24
GCST010321_110	PR interval	3.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004462	PR interval
EFO:0006917	spontaneous preterm birth
EFO:0006922	delivery measurement
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, affects cotreatment, increases expression	4
sodium arsenite	increases abundance, increases expression	2
Cadmium Chloride	increases expression, decreases expression, increases abundance	2
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
glycidyl methacrylate	increases expression	1
sodium arsenate	increases phosphorylation	1
beta-lapachone	increases expression	1
arsenite	affects localization	1
cobaltous chloride	increases expression	1
coumarin	increases phosphorylation	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Antimony	increases expression	1
Antimony Potassium Tartrate	increases expression	1
Arsenic	increases abundance, increases expression	1
Cadmium	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1

Cellosaurus cell lines

5 cell lines: 3 embryonic stem cell, 1 transformed cell line, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A0W5	SEES3-1V human DCP1A, clone1	Embryonic stem cell	Male
CVCL_A0W6	SEES3-1V human DCP1A, clone2	Embryonic stem cell	Male
CVCL_A0W7	SEES3-1V human DCP1A, clone3	Embryonic stem cell	Male
CVCL_B1AQ	Abcam HEK293 DCP1A KO	Transformed cell line	Female
CVCL_E0VH	Ubigene Huh-7 DCP1A KO	Cancer cell line	Male

Clinical trials (associated diseases)

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