DYDC1

Summary

DYDC1 (DPY30 domain containing 1, HGNC:23460) is a protein-coding gene on chromosome 10q23.1, encoding DPY30 domain-containing protein 1 (Q8WWB3). Functions as part of axonemal radial spoke complexes that play an important part in the motility of sperm and cilia.

This gene encodes a member of a family of proteins that contains a DPY30 domain. The encoded protein is involved in acrosome formation during spermatid development. This gene locus overlaps with a closely related gene on the opposite strand. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 143241 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_001269053

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23460
Approved symbol	DYDC1
Name	DPY30 domain containing 1
Location	10q23.1
Locus type	gene with protein product
Status	Approved
Aliases	bA36D19.5, DPY30D1
Ensembl gene	ENSG00000170788
Ensembl biotype	protein_coding
OMIM	615154
Entrez	143241

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000372202, ENST00000372204, ENST00000421924, ENST00000453477, ENST00000454362, ENST00000851664, ENST00000924050

RefSeq mRNA: 5 — MANE Select: NM_001269053 NM_001269053, NM_001370155, NM_001370156, NM_001370157, NM_138812

CCDS: CCDS7366

Canonical transcript exons

ENST00000372202 — 7 exons

Exon	Start	End
ENSE00001135953	80338467	80338571
ENSE00001164102	80339097	80339153
ENSE00001164109	80342269	80342361
ENSE00001164118	80351901	80352002
ENSE00001457174	80356712	80356755
ENSE00001457179	80352455	80352610
ENSE00001935518	80336105	80336185

Expression profiles

Bgee: expression breadth broad, 83 present calls, max score 96.94.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0965 / max 83.9018, expressed in 12 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
110361	0.0411	7
110359	0.0116	4
110356	0.0113	3
110357	0.0074	2
110353	0.0069	1
110354	0.0058	3
110360	0.0058	3
110355	0.0036	3
110358	0.0030	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	96.94	gold quality
right testis	UBERON:0004534	96.75	gold quality
testis	UBERON:0000473	93.69	gold quality
sperm	CL:0000019	89.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.25	gold quality
adult organism	UBERON:0007023	87.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.51	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	84.92	gold quality
bronchial epithelial cell	CL:0002328	82.92	gold quality
bronchus	UBERON:0002185	81.21	gold quality
right uterine tube	UBERON:0001302	78.08	gold quality
mucosa of paranasal sinus	UBERON:0005030	66.73	silver quality
nasal cavity mucosa	UBERON:0001826	63.27	gold quality
fallopian tube	UBERON:0003889	59.07	gold quality
oviduct epithelium	UBERON:0004804	57.84	gold quality
lower lobe of lung	UBERON:0008949	53.80	silver quality
corpus epididymis	UBERON:0004359	52.23	silver quality
caput epididymis	UBERON:0004358	51.83	silver quality
cauda epididymis	UBERON:0004360	50.06	gold quality
epithelium of nasopharynx	UBERON:0001951	47.30	silver quality
nasal cavity epithelium	UBERON:0005384	46.31	gold quality
buccal mucosa cell	CL:0002336	46.03	gold quality
endometrium	UBERON:0001295	45.71	gold quality
right lung	UBERON:0002167	44.99	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
left uterine tube	UBERON:0001303	42.08	gold quality
cortical plate	UBERON:0005343	41.73	gold quality
lung	UBERON:0002048	41.57	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.26

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	dydc2	ENSDARG00000101848
mus_musculus	Dydc1	ENSMUSG00000021790
rattus_norvegicus	Dydc1	ENSRNOG00000011165

Paralogs (1): DYDC2 (ENSG00000133665)

Protein

Protein identifiers

DPY30 domain-containing protein 1 — Q8WWB3 (reviewed: Q8WWB3)

All UniProt accessions (3): Q8WWB3, A0A0A0MSH3, X1WI33

UniProt curated annotations — full annotation on UniProt →

Function. Functions as part of axonemal radial spoke complexes that play an important part in the motility of sperm and cilia. Plays a crucial role during acrosome biogenesis.

Subunit / interactions. Component of the axonemal radial spoke complex 1 (RS1), at least composed of spoke head proteins RSPH1, RSPH3, RSPH9 and the cilia-specific component RSPH4A or sperm-specific component RSPH6A, spoke stalk proteins RSPH14, DNAJB13, DYDC1, ROPN1L and NME5, and the anchor protein IQUB. Interacts with SH3GL3.

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme.

Tissue specificity. Brain and testis. Accumulates during late stage of spermiogenesis.

Similarity. Belongs to the dpy-30 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WWB3-1	1	yes
Q8WWB3-2	2

RefSeq proteins (5): NP_001255982, NP_001357084, NP_001357085, NP_001357086, NP_620167 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007858	Dpy-30_motif	Conserved_site
IPR037856	Sdc1/DPY30	Family
IPR049630	DYDC-like_DD	Domain

Pfam: PF05186

UniProt features (2 total): chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WWB3-F1	83.93	0.65

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 41 (showing top): GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOCC_CYTOPLASMIC_REGION, GOCC_TRANSFERASE_COMPLEX, GOCC_SET1C_COMPASS_COMPLEX, GOCC_MOTILE_CILIUM, GOCC_HISTONE_METHYLTRANSFERASE_COMPLEX, GOCC_METHYLTRANSFERASE_COMPLEX, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, chr10q23, GOCC_9PLUS2_MOTILE_CILIUM, GSE13485_DAY3_VS_DAY7_YF17D_VACCINE_PBMC_UP, GOBP_MICROTUBULE_BASED_MOVEMENT, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS

GO Biological Process (0):

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

GO Cellular Component (7): radial spoke (GO:0001534), Set1C/COMPASS complex (GO:0048188), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
axoneme	1
protein-containing complex	1
histone methyltransferase complex	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

1277 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DYDC1	SH2D4B	Q5SQS7	686
DYDC1	TSPAN14	Q8NG11	634
DYDC1	SH3GL3	Q99963	572
DYDC1	TMEM61	Q8N0U2	571
DYDC1	CCSER2	Q9H7U1	555
DYDC1	LRRC43	Q8N309	517
DYDC1	FBXO47	Q5MNV8	513
DYDC1	ZMYND12	Q9H0C1	512
DYDC1	CFAP141	Q5VU69	506
DYDC1	SPMIP10	Q6ZNM6	488
DYDC1	ANKRD60	Q9BZ19	473
DYDC1	RAB42	Q8N4Z0	448
DYDC1	TMEM254	Q8TBM7	423
DYDC1	CFAP47	Q6ZTR5	412
DYDC1	FAM181A	Q8N9Y4	408

IntAct

136 interactions, top by confidence:

A	B	Type	Score
NME5	DYDC1	psi-mi:“MI:0915”(physical association)	0.830
DYDC1	NME5	psi-mi:“MI:0915”(physical association)	0.830
DYDC1	USHBP1	psi-mi:“MI:0915”(physical association)	0.780
USHBP1	DYDC1	psi-mi:“MI:0915”(physical association)	0.780
DYDC1	TXLNB	psi-mi:“MI:0915”(physical association)	0.720
TCHP	DYDC1	psi-mi:“MI:0915”(physical association)	0.720
TXLNB	DYDC1	psi-mi:“MI:0915”(physical association)	0.720
DYDC1	TCHP	psi-mi:“MI:0915”(physical association)	0.720
DYDC1	DPY30	psi-mi:“MI:0915”(physical association)	0.670
DPY30	DYDC1	psi-mi:“MI:0915”(physical association)	0.670
TFPT	DYDC1	psi-mi:“MI:0915”(physical association)	0.560
DYDC1	PIK3R2	psi-mi:“MI:0915”(physical association)	0.560
DYDC1	TXNDC9	psi-mi:“MI:0915”(physical association)	0.560
DYDC1	MOS	psi-mi:“MI:0915”(physical association)	0.560
DYDC1	CCNC	psi-mi:“MI:0915”(physical association)	0.560
DYDC1	CEP57L1	psi-mi:“MI:0915”(physical association)	0.560
ZGPAT	DYDC1	psi-mi:“MI:0915”(physical association)	0.560
WAC	DYDC1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (50): DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), TXLNB (Two-hybrid), CEP57L1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid), DYDC1 (Two-hybrid)

ESM2 similar proteins: A0A1C3NSL9, A1L3H4, A8BER9, A9ULR1, B9TQX4, J7MDG6, P0C745, P0C746, P0C747, P0CU43, P0CU44, P0CU51, P0CU52, P34433, P81834, P83960, P84576, P86794, Q08014, Q0WPZ7, Q0ZGT2, Q10043, Q14BU0, Q18012, Q28HK1, Q31TR2, Q329H0, Q32LH1, Q3E827, Q3YUQ0, Q4KLS8, Q6BEX5, Q6CBW0, Q6P5L7, Q6Y7W6, Q79669, Q7M3Y8, Q7TPW1, Q80HU9, Q8FAW3

Diamond homologs: Q2KIW3, Q32LH1, Q8WWB3, Q96IM9, Q9D9T0, Q6UBQ3

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
DYDC1	up-regulates	Acrosome_assembly
DYDC1	“up-regulates activity”	SH3GL3	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1343 predictions. Top by Δscore:

Variant	Effect	Δscore
10:80342362:C:CC	acceptor_gain	1.0000
10:80342371:C:CT	acceptor_gain	1.0000
10:80342372:A:T	acceptor_gain	1.0000
10:80338569:TTCC:T	acceptor_loss	0.9900
10:80338572:CTAC:C	acceptor_loss	0.9900
10:80338573:T:A	acceptor_loss	0.9900
10:80339150:TCTCC:T	acceptor_loss	0.9900
10:80339153:CCT:C	acceptor_loss	0.9900
10:80339154:CT:C	acceptor_loss	0.9900
10:80339155:T:C	acceptor_loss	0.9900
10:80342265:TTA:T	donor_loss	0.9900
10:80342266:TAC:T	donor_loss	0.9900
10:80342267:A:T	donor_loss	0.9900
10:80342268:C:CG	donor_loss	0.9900
10:80342272:G:A	donor_gain	0.9900
10:80342358:GTTG:G	acceptor_gain	0.9900
10:80342360:TG:T	acceptor_gain	0.9900
10:80342360:TGCTG:T	acceptor_loss	0.9900
10:80342362:C:G	acceptor_loss	0.9900
10:80344811:GAACT:G	donor_gain	0.9900
10:80344816:G:GG	donor_gain	0.9900
10:80338568:CTTC:C	acceptor_gain	0.9800
10:80338569:TTC:T	acceptor_gain	0.9800
10:80338572:C:CC	acceptor_gain	0.9800
10:80339151:CTC:C	acceptor_gain	0.9800
10:80342359:TTG:T	acceptor_gain	0.9800
10:80344814:CT:C	donor_gain	0.9800
10:80352453:A:AC	donor_gain	0.9800
10:80352454:C:CC	donor_gain	0.9800
10:80338465:A:AC	donor_gain	0.9700

AlphaMissense

1169 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:80352561:A:G	L14S	0.975
10:80352549:A:G	L18P	0.973
10:80352553:C:G	G17R	0.963
10:80352552:C:T	G17D	0.960
10:80352549:A:T	L18H	0.956
10:80352501:G:T	A34E	0.955
10:80352504:A:G	L33S	0.955
10:80338507:A:G	L155S	0.953
10:80352502:C:G	A34P	0.949
10:80352496:A:G	W36R	0.948
10:80352496:A:T	W36R	0.948
10:80352525:G:T	P26Q	0.944
10:80352538:C:G	A22P	0.943
10:80352585:A:G	L6P	0.935
10:80352547:C:G	A19P	0.929
10:80338530:G:C	S147R	0.920
10:80338530:G:T	S147R	0.920
10:80338532:T:G	S147R	0.920
10:80352549:A:C	L18R	0.920
10:80338513:G:T	P153H	0.917
10:80352526:G:A	P26S	0.914
10:80352525:G:C	P26R	0.912
10:80352508:A:C	Y32D	0.906
10:80338514:G:A	P153S	0.903
10:80352573:A:G	L10P	0.902
10:80352516:G:T	P29Q	0.900
10:80352540:A:T	V21E	0.895
10:80352585:A:T	L6H	0.884
10:80352519:T:C	D28G	0.883
10:80352507:T:G	Y32S	0.882

dbSNP variants (sampled 300 via entrez): RS1000073229 (10:80356223 T>C), RS1000448044 (10:80345037 C>A,T), RS1000545992 (10:80345784 A>G), RS1000682437 (10:80357962 T>G), RS1000749836 (10:80358683 G>A,C,T), RS1000877993 (10:80338685 T>A,C), RS1001049407 (10:80357955 C>A,G,T), RS1001191349 (10:80357680 C>A,T), RS1001660467 (10:80348599 G>A,C), RS1001714551 (10:80354956 A>G), RS1001937303 (10:80340336 G>A), RS1002006350 (10:80348862 A>G), RS1002099325 (10:80356447 C>A,G,T), RS1002181956 (10:80337024 G>C), RS1002327268 (10:80353821 T>C)

Disease associations

OMIM: gene MIM:615154 | 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
GCST008747_150	Estimated glomerular filtration rate	4.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
pirinixic acid	affects binding, decreases expression, increases activity	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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