CDADC1

Summary

CDADC1 (cytidine and dCMP deaminase domain containing 1, HGNC:20299) is a protein-coding gene on chromosome 13q14.2, encoding Cytidine and dCMP deaminase domain-containing protein 1 (Q9BWV3). Catalyzes the deamination of cytidine and deoxycytidine into uridine and deoxyuridine, respectively.

Enables several functions, including cytidine deaminase activity; importin-alpha family protein binding activity; and protein homodimerization activity. Involved in DNA cytosine deamination and cytidine deamination. Located in cytoplasm and nucleus.

Source: NCBI Gene 81602 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 63 total — 1 pathogenic
• MANE Select transcript: NM_030911

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20299
Approved symbol	CDADC1
Name	cytidine and dCMP deaminase domain containing 1
Location	13q14.2
Locus type	gene with protein product
Status	Approved
Aliases	NYD-SP15
Ensembl gene	ENSG00000102543
Ensembl biotype	protein_coding
OMIM	618997
Entrez	81602

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000251108, ENST00000429346, ENST00000466868, ENST00000484126, ENST00000496061, ENST00000496952, ENST00000948306

RefSeq mRNA: 2 — MANE Select: NM_030911 NM_001193478, NM_030911

CCDS: CCDS9415

Canonical transcript exons

ENST00000251108 — 10 exons

Exon	Start	End
ENSE00000836854	49280509	49280698
ENSE00000836858	49259346	49259523
ENSE00001097244	49291684	49293485
ENSE00001341844	49286222	49286282
ENSE00001611186	49274291	49274340
ENSE00001626516	49278350	49278519
ENSE00001917605	49247925	49248119
ENSE00003572349	49248871	49248965
ENSE00003602886	49267490	49268059
ENSE00003661517	49255839	49255913

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 96.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.3555 / max 269.9924, expressed in 1756 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135114	9.3555	1756

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.10	gold quality
male germ cell	CL:0000015	92.10	gold quality
secondary oocyte	CL:0000655	91.35	gold quality
tibia	UBERON:0000979	89.92	gold quality
left testis	UBERON:0004533	89.78	gold quality
right testis	UBERON:0004534	89.64	gold quality
tendon of biceps brachii	UBERON:0008188	88.11	gold quality
testis	UBERON:0000473	87.99	gold quality
endothelial cell	CL:0000115	87.87	gold quality
tendon	UBERON:0000043	86.70	gold quality
calcaneal tendon	UBERON:0003701	86.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.58	gold quality
sural nerve	UBERON:0015488	85.43	gold quality
Brodmann (1909) area 23	UBERON:0013554	85.23	gold quality
prefrontal cortex	UBERON:0000451	84.73	gold quality
left adrenal gland	UBERON:0001234	84.61	gold quality
middle temporal gyrus	UBERON:0002771	84.59	gold quality
bone marrow	UBERON:0002371	84.55	gold quality
left ovary	UBERON:0002119	84.44	gold quality
left adrenal gland cortex	UBERON:0035825	84.05	gold quality
parietal pleura	UBERON:0002400	83.99	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.97	gold quality
tibial nerve	UBERON:0001323	83.85	gold quality
adrenal gland	UBERON:0002369	83.82	gold quality
oocyte	CL:0000023	83.67	gold quality
left lobe of thyroid gland	UBERON:0001120	83.67	gold quality
anterior cingulate cortex	UBERON:0009835	83.62	gold quality
cingulate cortex	UBERON:0003027	83.50	gold quality
right ovary	UBERON:0002118	83.22	gold quality
primary visual cortex	UBERON:0002436	83.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting CDADC1, 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-4775	99.98	75.00	6394
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-3121-3P	99.82	71.96	3630
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-4679	99.76	69.19	1229

Literature-anchored findings (GeneRIF, showing 2)

• NYD-SP15 protein plays an important role in testicular development and spermatogenesis (PMID:16955368)
• NYD-SP15 contained nuclear localization sequence and nuclear export-signal and could dynamically shuttle between the nucleus and cytoplasm. (PMID:26945630)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdadc1	ENSDARG00000036650
mus_musculus	Cdadc1	ENSMUSG00000021982
rattus_norvegicus	Cdadc1	ENSRNOG00000012209

Paralogs (1): DCTD (ENSG00000129187)

Protein

Protein identifiers

Cytidine and dCMP deaminase domain-containing protein 1 — Q9BWV3 (reviewed: Q9BWV3)

Alternative names: Cytidine deaminase, Testis development protein NYD-SP15

All UniProt accessions (4): Q9BWV3, F2Z2H0, F2Z2J8, H0Y447

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the deamination of cytidine and deoxycytidine into uridine and deoxyuridine, respectively. May play an important role in testicular development and spermatogenesis.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Widely expressed. Expressed at high levels in the testis.

Similarity. Belongs to the cytidine and deoxycytidylate deaminase family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9BWV3-1	1	yes
Q9BWV3-2	2
Q9BWV3-3	3
Q9BWV3-4	4

RefSeq proteins (2): NP_001180407, NP_112173* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002125	CMP_dCMP_dom	Domain
IPR015517	dCMP_deaminase-rel	Family
IPR016192	APOBEC/CMP_deaminase_Zn-bd	Binding_site
IPR016193	Cytidine_deaminase-like	Homologous_superfamily
IPR035105	Deoxycytidylate_deaminase_dom	Domain

Pfam: PF00383

Catalyzed reactions (Rhea), 2 shown:

• 2’-deoxycytidine + H2O + H(+) = 2’-deoxyuridine + NH4(+) (RHEA:13433)
• cytidine + H2O + H(+) = uridine + NH4(+) (RHEA:16069)

UniProt features (24 total): binding site 6, splice variant 5, compositionally biased region 4, region of interest 3, domain 2, short sequence motif 2, chain 1, active site 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
9HFS	ELECTRON MICROSCOPY	2.8
9HFT	ELECTRON MICROSCOPY	2.9
9HFQ	ELECTRON MICROSCOPY	3.06
9HFR	ELECTRON MICROSCOPY	3.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BWV3-F1	79.53	0.62

Functional residue map

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

Catalytic / active sites (1): 400 (proton donor)

Ligand- & substrate-binding residues (6): 109; 134; 137; 398; 426; 429

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): GOBP_DNA_MODIFICATION, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, chr13q14, GOBP_DNA_METABOLIC_PROCESS, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_CARBON_NITROGEN_BUT_NOT_PEPTIDE_BONDS_IN_CYCLIC_AMIDINES, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_PROTEIN_HOMODIMERIZATION_ACTIVITY, GOMF_DEAMINASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_CARBON_NITROGEN_BUT_NOT_PEPTIDE_BONDS, MODULE_495, GOBP_DNA_DEAMINATION, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, GOBP_DNA_CYTOSINE_DEAMINATION, GOMF_CYTIDINE_DEAMINASE_ACTIVITY, GOMF_IMPORTIN_ALPHA_FAMILY_PROTEIN_BINDING

GO Biological Process (1): DNA cytosine deamination (GO:0070383)

GO Molecular Function (8): cytidine deaminase activity (GO:0004126), dCMP deaminase activity (GO:0004132), zinc ion binding (GO:0008270), protein homodimerization activity (GO:0042803), importin-alpha family protein binding (GO:0061676), catalytic activity (GO:0003824), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	2
deaminase activity	2
DNA deamination	1
transition metal ion binding	1
identical protein binding	1
protein dimerization activity	1
protein binding	1
molecular_function	1
catalytic activity	1
cation binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

660 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDADC1	FNDC3A	Q9Y2H6	649
CDADC1	CAB39L	Q9H9S4	646
CDADC1	SETDB2	Q96T68	628
CDADC1	RCBTB1	Q8NDN9	598
CDADC1	MLNR	O43193	589
CDADC1	CCDC83	Q8IWF9	583
CDADC1	PHF11	Q9UIL8	574
CDADC1	RCBTB2	O95199	517
CDADC1	DCTD	P32321	514
CDADC1	CYSLTR2	Q9NS75	492
CDADC1	ARL11	Q969Q4	476
CDADC1	DRC9	Q9H095	446
CDADC1	ITM2B	Q9Y287	444
CDADC1	NHLRC2	Q8NBF2	442
CDADC1	CCDC186	Q7Z3E2	438

IntAct

12 interactions, top by confidence:

A	B	Type	Score
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
CDADC1	H1-1	psi-mi:“MI:0915”(physical association)	0.400
CDADC1	BLTP3B	psi-mi:“MI:0915”(physical association)	0.000
IFFO1	CDADC1	psi-mi:“MI:0915”(physical association)	0.000
AMOTL1	CDADC1	psi-mi:“MI:0915”(physical association)	0.000
COBLL1	CDADC1	psi-mi:“MI:0915”(physical association)	0.000
HMBOX1	CDADC1	psi-mi:“MI:0915”(physical association)	0.000
TLK2	CDADC1	psi-mi:“MI:0915”(physical association)	0.000
DDHD1	CDADC1	psi-mi:“MI:0915”(physical association)	0.000
SCML1	CDADC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): CDADC1 (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), CDADC1 (Proximity Label-MS), CDADC1 (Affinity Capture-MS), CDADC1 (Affinity Capture-MS), H2AFX (Cross-Linking-MS (XL-MS)), CDADC1 (Proximity Label-MS)

ESM2 similar proteins: A0A2R8VHF7, A0JM23, A2QRA0, A4IIA7, A4IIV4, A6NFN9, A6NHR9, A7MBF6, F4IG73, F4JSE7, O17482, O95876, P12540, P21784, P34089, P38899, P55895, P56696, Q08AW4, Q0D2D7, Q12789, Q13829, Q28DC9, Q2WGJ8, Q3E7Y5, Q3UUE9, Q4R907, Q4VXA5, Q5BK83, Q5EA90, Q5F476, Q5HZS2, Q5M9F0, Q5RAX4, Q5RBH4, Q5RD21, Q6AYL6, Q6DGA7, Q6PIY5, Q70XZ2

Diamond homologs: O22000, P00814, P16006, P30648, P32321, P32393, P33968, Q4R683, Q5M9G0, Q5RAX4, Q5RC69, Q5U3U4, Q8BMD5, Q8K2D6, Q9BWV3, Q9VWA2, O43012, P06773

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	43
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1527766	GRCh37/hg19 13q13.3-31.1(chr13:36376204-80681753)	Pathogenic

SpliceAI

2279 predictions. Top by Δscore:

Variant	Effect	Δscore
13:49248115:GACCG:G	donor_gain	1.0000
13:49248118:CGGT:C	donor_loss	1.0000
13:49248120:G:C	donor_loss	1.0000
13:49248120:G:GG	donor_gain	1.0000
13:49248121:T:G	donor_loss	1.0000
13:49255822:AATCT:A	acceptor_gain	1.0000
13:49255826:T:TA	acceptor_gain	1.0000
13:49255836:TAGAA:T	acceptor_loss	1.0000
13:49255837:A:AG	acceptor_gain	1.0000
13:49255837:A:AT	acceptor_loss	1.0000
13:49255838:G:GG	acceptor_gain	1.0000
13:49255838:G:T	acceptor_loss	1.0000
13:49255838:GA:G	acceptor_gain	1.0000
13:49255838:GAA:G	acceptor_gain	1.0000
13:49255838:GAAA:G	acceptor_gain	1.0000
13:49255909:GACAG:G	donor_gain	1.0000
13:49255910:ACAG:A	donor_loss	1.0000
13:49255911:CAGGT:C	donor_loss	1.0000
13:49255912:AGGTA:A	donor_loss	1.0000
13:49255913:GG:G	donor_loss	1.0000
13:49255914:G:GC	donor_loss	1.0000
13:49255915:T:G	donor_loss	1.0000
13:49267488:A:AG	acceptor_gain	1.0000
13:49267489:G:GG	acceptor_gain	1.0000
13:49278348:A:AG	acceptor_gain	1.0000
13:49278349:G:GG	acceptor_gain	1.0000
13:49278349:GA:G	acceptor_gain	1.0000
13:49278349:GAGAA:G	acceptor_gain	1.0000
13:49278516:TTAGG:T	donor_loss	1.0000
13:49278519:GGTA:G	donor_loss	1.0000

AlphaMissense

3432 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:49248915:A:C	S43R	0.999
13:49248917:C:A	S43R	0.999
13:49248917:C:G	S43R	0.999
13:49267513:T:A	W152R	0.999
13:49267513:T:C	W152R	0.999
13:49259362:T:C	L90P	0.998
13:49259482:C:T	S130F	0.998
13:49274314:G:C	A342P	0.998
13:49278400:T:A	N367K	0.998
13:49278400:T:G	N367K	0.998
13:49278476:T:C	F393L	0.998
13:49278478:C:A	F393L	0.998
13:49278478:C:G	F393L	0.998
13:49278491:C:G	H398D	0.998
13:49259434:C:A	A114D	0.997
13:49259473:T:C	L127P	0.997
13:49259475:T:G	Y128D	0.997
13:49259482:C:A	S130Y	0.997
13:49259485:G:T	R131I	0.997
13:49259491:C:A	P133Q	0.997
13:49268054:G:C	R332P	0.997
13:49274293:G:C	D335H	0.997
13:49274311:G:T	G341W	0.997
13:49274318:T:A	V343D	0.997
13:49274323:T:A	W345R	0.997
13:49274323:T:C	W345R	0.997
13:49278493:T:A	H398Q	0.997
13:49278493:T:G	H398Q	0.997
13:49278502:G:C	Q401H	0.997
13:49278502:G:T	Q401H	0.997

dbSNP variants (sampled 300 via entrez): RS1000008698 (13:49272501 G>C), RS1000110453 (13:49280210 G>T), RS1000215895 (13:49263673 T>C), RS1000300808 (13:49264889 T>G), RS1000317075 (13:49287878 G>A), RS1000400033 (13:49272895 C>T), RS1000410645 (13:49280228 T>A), RS1000524910 (13:49279832 C>A), RS1000670335 (13:49250519 G>A), RS1000685122 (13:49273315 C>A,T), RS1000770549 (13:49265809 A>C), RS1000854347 (13:49287036 C>T), RS1000935726 (13:49287480 A>ATCTC,ATCTG,ATCTT), RS1001019347 (13:49293857 G>T), RS1001120741 (13:49255619 A>G)

Disease associations

OMIM: gene MIM:618997 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases methylation, affects cotreatment, increases expression	5
Benzo(a)pyrene	decreases methylation, increases expression	3
sodium arsenite	increases abundance, increases expression, affects expression, affects cotreatment	2
Acetaminophen	increases expression	2
Arsenic	affects expression, affects cotreatment, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Urethane	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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