DPCD

Summary

DPCD (deleted in primary ciliary dyskinesia homolog (mouse), HGNC:24542) is a protein-coding gene on chromosome 10q24.32, encoding Protein DPCD (Q9BVM2). May play a role in the formation or function of ciliated cells.

This gene in mouse encodes a protein that may be involved in the generation and maintenance of ciliated cells. In mouse, expression of this gene increases during ciliated cell differentiation, and disruption of this gene has been linked to primary ciliary dyskinesia.

Source: NCBI Gene 25911 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 46 total
• MANE Select transcript: NM_015448

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24542
Approved symbol	DPCD
Name	deleted in primary ciliary dyskinesia homolog (mouse)
Location	10q24.32
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP566F084, RP11-529I10.4
Ensembl gene	ENSG00000166171
Ensembl biotype	protein_coding
OMIM	616467
Entrez	25911

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 14 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000370147, ENST00000370151, ENST00000434727, ENST00000470165, ENST00000475443, ENST00000626968, ENST00000897436, ENST00000897437, ENST00000897438, ENST00000897439, ENST00000897440, ENST00000927874, ENST00000927875, ENST00000927876, ENST00000927877, ENST00000927878

RefSeq mRNA: 5 — MANE Select: NM_015448 NM_001329742, NM_001329743, NM_001329744, NM_001329745, NM_015448

CCDS: CCDS7514, CCDS86141

Canonical transcript exons

ENST00000370151 — 6 exons

Exon	Start	End
ENSE00001100436	101600738	101600862
ENSE00001100439	101608835	101608937
ENSE00001859286	101588321	101588400
ENSE00001953044	101609367	101609662
ENSE00003496444	101601203	101601336
ENSE00003661578	101594658	101594738

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 98.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.3460 / max 199.4382, expressed in 1708 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
106670	11.3460	1708

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.28	gold quality
right testis	UBERON:0004534	98.16	gold quality
sperm	CL:0000019	97.59	gold quality
right uterine tube	UBERON:0001302	97.51	gold quality
bronchial epithelial cell	CL:0002328	97.06	gold quality
testis	UBERON:0000473	96.85	gold quality
bronchus	UBERON:0002185	96.31	gold quality
pancreatic ductal cell	CL:0002079	95.58	gold quality
adenohypophysis	UBERON:0002196	95.09	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.09	gold quality
pituitary gland	UBERON:0000007	94.83	gold quality
adult organism	UBERON:0007023	93.30	gold quality
anterior cingulate cortex	UBERON:0009835	93.20	gold quality
islet of Langerhans	UBERON:0000006	93.13	gold quality
nucleus accumbens	UBERON:0001882	92.96	gold quality
hypothalamus	UBERON:0001898	92.94	gold quality
amygdala	UBERON:0001876	92.87	gold quality
left ventricle myocardium	UBERON:0006566	92.53	silver quality
caudate nucleus	UBERON:0001873	92.18	gold quality
right frontal lobe	UBERON:0002810	91.94	gold quality
tibialis anterior	UBERON:0001385	91.89	silver quality
putamen	UBERON:0001874	91.75	gold quality
prefrontal cortex	UBERON:0000451	91.70	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.53	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.06	gold quality
apex of heart	UBERON:0002098	90.96	gold quality
right lobe of thyroid gland	UBERON:0001119	90.50	gold quality
left lobe of thyroid gland	UBERON:0001120	90.43	gold quality
heart left ventricle	UBERON:0002084	90.21	gold quality
neocortex	UBERON:0001950	90.07	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	26.41
E-CURD-114	yes	11.82
E-MTAB-6075	no	239.63
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• The mouse homolog of this gene (named Dpcd, for Deleted in a mouse model of Primary Ciliary Dyskinesia) appears to be responsible for an inner arm defect in cilia. (PMID:14630615)
• a novel candidate gene for primary ciliary dyskinesia (PMID:14630615)
• Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. (PMID:35901867)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	dpcd	ENSDARG00000060501
mus_musculus	Dpcd	ENSMUSG00000041035
rattus_norvegicus	Dpcd	ENSRNOG00000017241
drosophila_melanogaster	CG13901	FBGN0035164

Protein

Protein identifiers

Protein DPCD — Q9BVM2 (reviewed: Q9BVM2)

All UniProt accessions (3): Q9BVM2, Q5JQQ2, Q5JQQ4

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the formation or function of ciliated cells.

Tissue specificity. Highly expressed in the testis. Weakly expressed in pancreas, skeletal muscle and heart. Expression increases during ciliated cell differentiation.

Similarity. Belongs to the DPCD family.

RefSeq proteins (5): NP_001316671, NP_001316672, NP_001316673, NP_001316674, NP_056263* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026224	DPCD	Family

Pfam: PF14913

UniProt features (4 total): sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BVM2-F1	90.21	0.79

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 136 (showing top): CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MENSE_HYPOXIA_UP, GOBP_MALE_GAMETE_GENERATION, GOBP_VENTRICULAR_SYSTEM_DEVELOPMENT, CAGCTG_AP4_Q5, GOBP_FOREBRAIN_DEVELOPMENT, GOBP_SPECIFICATION_OF_SYMMETRY, IRF7_01, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_HEAD_DEVELOPMENT, GOBP_LATERAL_VENTRICLE_DEVELOPMENT, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_TELENCEPHALON_DEVELOPMENT

GO Biological Process (9): epithelial cilium movement involved in extracellular fluid movement (GO:0003351), spermatogenesis (GO:0007283), determination of left/right symmetry (GO:0007368), lateral ventricle development (GO:0021670), third ventricle development (GO:0021678), flagellated sperm motility (GO:0030317), establishment of localization in cell (GO:0051649), ventricular system development (GO:0021591), left/right pattern formation (GO:0060972)

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

GO Cellular Component (2): extracellular region (GO:0005576), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ventricular system development	2
anatomical structure development	2
cilium movement	1
extracellular transport	1
microtubule-based transport	1
developmental process involved in reproduction	1
male gamete generation	1
determination of bilateral symmetry	1
left/right pattern formation	1
telencephalon development	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
establishment of localization	1
cellular localization	1
brain development	1
system development	1
regionalization	1
binding	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

420 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DPCD	DNAAF10	Q96MX6	660
DPCD	STK36	Q9NRP7	610
DPCD	AK7	Q96M32	568
DPCD	RTTN	Q86VV8	491
DPCD	SPAG6	O75602	484
DPCD	KIF27	Q86VH2	479
DPCD	PKD1L1	Q8TDX9	461
DPCD	POLL	Q9UGP5	447
DPCD	DRICH1	Q6PGQ1	433
DPCD	DCAF8L1	A6NGE4	430
DPCD	AK8	Q96MA6	416
DPCD	DCAF8L2	P0C7V8	399
DPCD	DYNC2I2	Q96EX3	388
DPCD	TTLL1	O95922	380
DPCD	MSGN1	A6NI15	379

IntAct

47 interactions, top by confidence:

A	B	Type	Score
LSM3	LSM1	psi-mi:“MI:0914”(association)	0.950
RUVBL2	DPCD	psi-mi:“MI:0915”(physical association)	0.940
DPCD	RUVBL2	psi-mi:“MI:0915”(physical association)	0.940
RUVBL1	ZNHIT1	psi-mi:“MI:0914”(association)	0.860
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
RUVBL2	POLR3A	psi-mi:“MI:0914”(association)	0.640
RUVBL1	POLR3A	psi-mi:“MI:0914”(association)	0.640
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
RABGGTA	YKT6	psi-mi:“MI:0914”(association)	0.530
MYBPHL	DPCD	psi-mi:“MI:0915”(physical association)	0.400
DPCD	CDC37	psi-mi:“MI:0915”(physical association)	0.400
Ruvbl1	AAR2	psi-mi:“MI:0914”(association)	0.350
Ruvbl2	TTI2	psi-mi:“MI:0914”(association)	0.350
Lin7c	AMOTL2	psi-mi:“MI:0914”(association)	0.350
RAB18	ASDURF	psi-mi:“MI:0914”(association)	0.350
RUVBL2	ASDURF	psi-mi:“MI:0914”(association)	0.350
RUVBL1	ASDURF	psi-mi:“MI:0914”(association)	0.350

BioGRID (54): DPCD (Two-hybrid), DPCD (Two-hybrid), DPCD (Proximity Label-MS), DPCD (Proximity Label-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS), DPCD (Affinity Capture-MS)

ESM2 similar proteins: A0A4X1TB62, A2AGL3, A8YXY3, D3ZV31, E9PZQ0, F1LMY4, O60613, O75817, P0CL18, P11716, P16960, P21817, P41214, P46718, P47224, P47816, P50747, P55884, Q08326, Q0II25, Q0IIH8, Q0PNE2, Q16342, Q1JQA1, Q24K21, Q3UX43, Q4G061, Q4R528, Q58CR3, Q5PPG7, Q5R7U7, Q5RA63, Q6AYM4, Q6NYU2, Q80YV4, Q8BKW4, Q8BPA8, Q8CBY8, Q8JZQ9, Q91W86

Diamond homologs: A4IHF8, A5D8N2, Q0P448, Q24K21, Q6AYM4, Q8BPA8, Q9BVM2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 38 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.

GO biological processes:

GO term	Partners	Fold	FDR
protein stabilization	7	13.4×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2754 predictions. Top by Δscore:

Variant	Effect	Δscore
10:101582761:A:AC	donor_gain	1.0000
10:101582762:C:CC	donor_gain	1.0000
10:101582762:CTGT:C	donor_gain	1.0000
10:101582789:C:A	donor_gain	1.0000
10:101582803:T:A	donor_gain	1.0000
10:101582891:CCT:C	acceptor_loss	1.0000
10:101582892:C:G	acceptor_loss	1.0000
10:101582893:T:G	acceptor_loss	1.0000
10:101583522:T:C	donor_gain	1.0000
10:101583546:C:A	donor_gain	1.0000
10:101583586:A:AC	donor_gain	1.0000
10:101583587:C:CC	donor_gain	1.0000
10:101584920:C:CC	acceptor_gain	1.0000
10:101584921:T:C	acceptor_gain	1.0000
10:101584921:T:TC	acceptor_gain	1.0000
10:101585864:A:AC	donor_gain	1.0000
10:101585865:C:CC	donor_gain	1.0000
10:101586153:CACT:C	acceptor_gain	1.0000
10:101600736:A:AG	acceptor_gain	1.0000
10:101600737:G:GG	acceptor_gain	1.0000
10:101600849:A:T	donor_gain	1.0000
10:101601332:AAGAA:A	donor_gain	1.0000
10:101601333:AGAA:A	donor_gain	1.0000
10:101601334:GAA:G	donor_gain	1.0000
10:101601334:GAAG:G	donor_gain	1.0000
10:101601335:AA:A	donor_gain	1.0000
10:101601335:AAGTG:A	donor_loss	1.0000
10:101601336:AG:A	donor_loss	1.0000
10:101601337:G:GG	donor_gain	1.0000
10:101601337:GTG:G	donor_loss	1.0000

AlphaMissense

1338 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:101600782:T:A	W64R	0.997
10:101600782:T:C	W64R	0.997
10:101601242:T:A	W104R	0.997
10:101601242:T:C	W104R	0.997
10:101601246:G:C	R105P	0.996
10:101608927:T:C	L166P	0.996
10:101600741:G:C	R50T	0.995
10:101600742:A:C	R50S	0.995
10:101600742:A:T	R50S	0.995
10:101601318:T:A	V129D	0.995
10:101600750:G:C	R53P	0.994
10:101600784:G:C	W64C	0.994
10:101600784:G:T	W64C	0.994
10:101594702:G:C	A37P	0.992
10:101594670:T:A	V26D	0.991
10:101594675:T:G	Y28D	0.989
10:101600741:G:T	R50I	0.989
10:101601252:G:C	R107P	0.989
10:101601278:T:G	Y116D	0.989
10:101588352:T:A	W6R	0.988
10:101588352:T:C	W6R	0.988
10:101609367:T:G	Y170D	0.988
10:101601249:T:A	I106N	0.987
10:101608933:T:A	I168N	0.987
10:101601258:T:C	L109P	0.986
10:101608836:T:G	Y136D	0.986
10:101609375:G:C	K172N	0.986
10:101609375:G:T	K172N	0.986
10:101594711:T:G	Y40D	0.985
10:101594672:C:G	H27D	0.984

dbSNP variants (sampled 300 via entrez): RS1000129686 (10:101593160 G>A), RS1000153970 (10:101607599 T>C), RS1000163331 (10:101593209 C>G,T), RS1000182354 (10:101606128 C>A), RS1000208148 (10:101607981 C>T), RS1000354698 (10:101586782 A>C), RS1000487268 (10:101605617 A>T), RS1000618098 (10:101606488 T>A), RS1000645496 (10:101598732 C>T), RS1000758849 (10:101591963 G>A), RS1000992457 (10:101606285 C>T), RS1001012227 (10:101587069 T>C), RS1001187033 (10:101587593 G>T), RS1001191258 (10:101592215 A>G), RS1001219678 (10:101604513 T>G)

Disease associations

OMIM: gene MIM:616467 | 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
GCST90002392_547	Mean corpuscular volume	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	5
Cyclosporine	decreases expression, increases expression	2
methylmercuric chloride	decreases expression	1
bisphenol A	affects expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	decreases expression	1
benzo(e)pyrene	decreases methylation	1
Temozolomide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Atrazine	decreases expression	1
Doxorubicin	increases expression	1
Ivermectin	decreases expression	1
Ketoconazole	increases expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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