DYDC2

Summary

DYDC2 (DPY30 domain containing 2, HGNC:23468) is a protein-coding gene on chromosome 10q23.1, encoding DPY30 domain-containing protein 2 (Q96IM9).

This gene encodes a member of a family of proteins that contains a DPY30 domain. This gene locus overlaps with a closely related gene on the opposite strand. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 84332 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 27 total
• MANE Select transcript: NM_032372

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23468
Approved symbol	DYDC2
Name	DPY30 domain containing 2
Location	10q23.1
Locus type	gene with protein product
Status	Approved
Aliases	bA36D19.6, MGC16186
Ensembl gene	ENSG00000133665
Ensembl biotype	protein_coding
Entrez	84332

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 20 protein_coding

ENST00000256039, ENST00000372197, ENST00000372198, ENST00000372199, ENST00000411538, ENST00000444807, ENST00000616870, ENST00000873813, ENST00000873814, ENST00000924169, ENST00000924170, ENST00000924171, ENST00000924172, ENST00000924173, ENST00000924174, ENST00000924175, ENST00000924176, ENST00000924177, ENST00000924178, ENST00000969730

RefSeq mRNA: 3 — MANE Select: NM_032372 NM_001270041, NM_001270042, NM_032372

CCDS: CCDS58088, CCDS7367

Canonical transcript exons

ENST00000256039 — 5 exons

Exon	Start	End
ENSE00000909302	80362951	80363073
ENSE00001383755	80366688	80368073
ENSE00001429202	80357893	80358045
ENSE00001432655	80356781	80356825
ENSE00003672024	80362435	80362590

Expression profiles

Bgee: expression breadth ubiquitous, 143 present calls, max score 98.50.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1695 / max 20.4837, expressed in 77 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105853	0.1695	77

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	98.50	gold quality
bronchial epithelial cell	CL:0002328	94.64	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.00	gold quality
bronchus	UBERON:0002185	92.75	gold quality
oviduct epithelium	UBERON:0004804	86.34	gold quality
fallopian tube	UBERON:0003889	83.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.31	gold quality
mucosa of paranasal sinus	UBERON:0005030	82.10	gold quality
left testis	UBERON:0004533	77.43	gold quality
right testis	UBERON:0004534	76.94	gold quality
nucleus accumbens	UBERON:0001882	75.26	gold quality
testis	UBERON:0000473	74.59	gold quality
caudate nucleus	UBERON:0001873	72.89	gold quality
nasopharynx	UBERON:0001728	72.71	silver quality
epithelium of nasopharynx	UBERON:0001951	72.71	silver quality
ventricular zone	UBERON:0003053	70.71	gold quality
nasal cavity mucosa	UBERON:0001826	69.23	gold quality
hypothalamus	UBERON:0001898	68.87	gold quality
cortical plate	UBERON:0005343	68.69	gold quality
anterior cingulate cortex	UBERON:0009835	68.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.50	gold quality
amygdala	UBERON:0001876	68.07	gold quality
prefrontal cortex	UBERON:0000451	67.49	gold quality
right lung	UBERON:0002167	67.15	gold quality
left uterine tube	UBERON:0001303	64.57	gold quality
putamen	UBERON:0001874	63.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	63.76	gold quality
ganglionic eminence	UBERON:0004023	63.56	gold quality
Ammon’s horn	UBERON:0001954	62.66	gold quality
nasal cavity epithelium	UBERON:0005384	61.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-130148	yes	11.59
E-ANND-3	yes	10.71
E-MTAB-9388	yes	6.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting DYDC2, 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-4682	100.00	68.89	1258
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-4666A-5P	99.41	69.72	1887

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	dydc2	ENSDARG00000101848
mus_musculus	Dydc2	ENSMUSG00000021791
rattus_norvegicus	Dydc2	ENSRNOG00000039591

Paralogs (1): DYDC1 (ENSG00000170788)

Protein

Protein identifiers

DPY30 domain-containing protein 2 — Q96IM9 (reviewed: Q96IM9)

All UniProt accessions (3): A0A0A0MRQ7, Q96IM9, X1WI30

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the dpy-30 family.

RefSeq proteins (3): NP_001256970, NP_001256971, NP_115748* (*=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, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96IM9-F1	72.17	0.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, EFC_Q6, MODULE_95, GOCC_CYTOPLASMIC_REGION, GOCC_TRANSFERASE_COMPLEX, GOCC_SET1C_COMPASS_COMPLEX, GOCC_HISTONE_METHYLTRANSFERASE_COMPLEX, GOCC_METHYLTRANSFERASE_COMPLEX, RFX1_01, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, chr10q23, HATADA_METHYLATED_IN_LUNG_CANCER_UP, MODULE_163

GO Biological Process (0):

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

GO Cellular Component (1): Set1C/COMPASS complex (GO:0048188)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
histone methyltransferase complex	1

Protein interactions and networks

STRING

897 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DYDC2	SH2D4B	Q5SQS7	645
DYDC2	TSPAN14	Q8NG11	611
DYDC2	CIBAR2	Q6ZTR7	604
DYDC2	ODAD4	Q96NG3	509
DYDC2	TMEM61	Q8N0U2	507
DYDC2	CCSER2	Q9H7U1	483
DYDC2	GHITM	Q9H3K2	446
DYDC2	ZCCHC24	Q8N2G6	440
DYDC2	MAGEL2	Q9UJ55	419
DYDC2	RAB42	Q8N4Z0	417
DYDC2	OCEL1	Q9H607	415
DYDC2	TMEM254	Q8TBM7	381
DYDC2	FAM156A	Q8NDB6	380
DYDC2	MS4A15	Q8N5U1	377
DYDC2	PON1	P27169	371

IntAct

20 interactions, top by confidence:

A	B	Type	Score
DYDC2	NME5	psi-mi:“MI:0915”(physical association)	0.790
NME5	DYDC2	psi-mi:“MI:0915”(physical association)	0.790
POLR1A	DYDC2	psi-mi:“MI:0915”(physical association)	0.560
DYDC2	DPY30	psi-mi:“MI:0915”(physical association)	0.560
TENT5D	DYDC2	psi-mi:“MI:0915”(physical association)	0.560
UBXN2A	DYDC2	psi-mi:“MI:0915”(physical association)	0.560
DYDC2	INPPL1	psi-mi:“MI:0914”(association)	0.560
INPPL1	DYDC2	psi-mi:“MI:0915”(physical association)	0.560
SCRIB	CHD2	psi-mi:“MI:0914”(association)	0.350
POLR1A	DYDC2	psi-mi:“MI:0915”(physical association)	0.000
DPY30	DYDC2	psi-mi:“MI:0915”(physical association)	0.000
UBXN2A	DYDC2	psi-mi:“MI:0915”(physical association)	0.000
TENT5D	DYDC2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): DYDC2 (Two-hybrid), DYDC2 (Two-hybrid), DPY30 (Two-hybrid), UBXN2A (Two-hybrid), FAM46D (Two-hybrid), ARHGEF12 (Affinity Capture-MS), DLGAP5 (Affinity Capture-MS), NME5 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), INPPL1 (Affinity Capture-MS), TGFBRAP1 (Affinity Capture-MS), NEDD8-MDP1 (Affinity Capture-MS), DYDC2 (Two-hybrid)

ESM2 similar proteins: A1L2Y1, A2A3V1, A2AFS9, A4FU69, A6NMK8, A7E3D8, A8MT70, A8T6P4, A9JRX0, B0CM36, B7ZS37, D3Z6S9, O95447, P70347, Q0P5X1, Q0P5X5, Q14B48, Q2KHM9, Q2KIW3, Q3TCJ8, Q3V036, Q4R3Q7, Q5CZC0, Q5MY90, Q5PQS2, Q5R9L2, Q5RHB5, Q5T1N1, Q5XI03, Q62394, Q6A000, Q6GQV1, Q6NZK5, Q6ZRS4, Q6ZVD7, Q70YC5, Q7Z572, Q86T90, Q8BG89, Q8BVV7

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	3
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1314 predictions. Top by Δscore:

Variant	Effect	Δscore
10:80362430:TCCA:T	acceptor_loss	1.0000
10:80362433:A:AC	acceptor_loss	1.0000
10:80362433:A:AG	acceptor_gain	1.0000
10:80362434:G:C	acceptor_loss	1.0000
10:80362434:G:GA	acceptor_gain	1.0000
10:80362434:GGC:G	acceptor_gain	1.0000
10:80362434:GGCT:G	acceptor_gain	1.0000
10:80366682:A:AG	acceptor_gain	1.0000
10:80366684:TTAGG:T	acceptor_loss	1.0000
10:80366686:A:AG	acceptor_gain	1.0000
10:80366686:AGG:A	acceptor_loss	1.0000
10:80366687:G:GC	acceptor_gain	1.0000
10:80366687:GGAAC:G	acceptor_gain	1.0000
10:80344811:GAACT:G	donor_gain	0.9900
10:80344816:G:GG	donor_gain	0.9900
10:80362432:CAGG:C	acceptor_gain	0.9900
10:80362433:AG:A	acceptor_gain	0.9900
10:80362433:AGGC:A	acceptor_gain	0.9900
10:80362433:AGGCT:A	acceptor_gain	0.9900
10:80362434:GG:G	acceptor_gain	0.9900
10:80362434:GGCTG:G	acceptor_gain	0.9900
10:80362505:TGGCG:T	donor_gain	0.9900
10:80362566:G:GT	donor_gain	0.9900
10:80362567:A:T	donor_gain	0.9900
10:80362950:GA:G	acceptor_gain	0.9900
10:80362950:GAAT:G	acceptor_gain	0.9900
10:80362950:GAATA:G	acceptor_gain	0.9900
10:80363032:G:GT	donor_gain	0.9900
10:80363069:ACAAG:A	donor_loss	0.9900
10:80363070:CAAGG:C	donor_loss	0.9900

AlphaMissense

1189 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:80362519:C:T	P26S	0.939
10:80362538:A:C	Y32S	0.923
10:80362492:G:C	A17P	0.922
10:80362493:C:A	A17E	0.922
10:80362541:T:C	L33P	0.922
10:80362520:C:A	P26H	0.918
10:80362537:T:G	Y32D	0.916
10:80362543:G:C	A34P	0.911
10:80362553:T:C	L37P	0.905
10:80362475:G:T	G11V	0.897
10:80362520:C:G	P26R	0.896
10:80362496:T:C	L18P	0.894
10:80362544:C:A	A34D	0.891
10:80362519:C:A	P26T	0.889
10:80362529:C:A	P29Q	0.887
10:80362507:G:C	A22P	0.879
10:80362526:A:G	D28G	0.872
10:80362498:G:C	A19P	0.871
10:80362448:A:T	E2V	0.870
10:80362537:T:C	Y32H	0.866
10:80362520:C:T	P26L	0.865
10:80362460:T:C	L6P	0.859
10:80362475:G:A	G11E	0.852
10:80362541:T:A	L33Q	0.847
10:80362538:A:G	Y32C	0.834
10:80362541:T:G	L33R	0.834
10:80362496:T:A	L18Q	0.832
10:80362484:T:A	L14Q	0.831
10:80362529:C:G	P29R	0.828
10:80362484:T:C	L14P	0.822

dbSNP variants (sampled 300 via entrez): RS1000073229 (10:80356223 T>C), RS1000183720 (10:80363233 A>G,T), RS1000255872 (10:80362917 G>A,T), RS1000399455 (10:80363405 A>G), RS1000448044 (10:80345037 C>A,T), RS1000453556 (10:80365882 T>A), RS1000545992 (10:80345784 A>G), RS1000582461 (10:80367986 C>T), RS1000682437 (10:80357962 T>G), RS1000735151 (10:80362045 T>C), RS1000749836 (10:80358683 G>A,C,T), RS1000794872 (10:80367368 G>A), RS1000976061 (10:80367637 C>G,T), RS1001049407 (10:80357955 C>A,G,T), RS1001182465 (10:80365080 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005542_5	Sarcoidosis (non-Lofgren’s syndrome without extrapulmonary manifestations)	4.000000e-06
GCST008747_24	Estimated glomerular filtration rate	6.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cyclosporine	increases expression	2
dicrotophos	decreases expression	1
propionaldehyde	increases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
ethyl-p-hydroxybenzoate	decreases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	increases methylation	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Aldehydes	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression, increases methylation	1
Okadaic Acid	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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