CNTD1

Summary

CNTD1 (cyclin N-terminal domain containing 1, HGNC:26847) is a protein-coding gene on chromosome 17q21.2-q21.31, encoding Cyclin N-terminal domain-containing protein 1 (Q8N815). Plays a role in the different steps of crossover formation during meiotic recombination.

Predicted to be involved in reciprocal meiotic recombination and regulation of meiotic cell cycle. Predicted to act upstream of or within spermatogenesis. Predicted to be located in chromosome. Predicted to be active in site of double-strand break.

Source: NCBI Gene 124817 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_173478

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26847
Approved symbol	CNTD1
Name	cyclin N-terminal domain containing 1
Location	17q21.2-q21.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40137
Ensembl gene	ENSG00000176563
Ensembl biotype	protein_coding
OMIM	618166
Entrez	124817

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000315066, ENST00000585355, ENST00000586652, ENST00000588408, ENST00000588527, ENST00000591559, ENST00000592166

RefSeq mRNA: 2 — MANE Select: NM_173478 NM_001330222, NM_173478

CCDS: CCDS11440, CCDS82131

Canonical transcript exons

ENST00000588408 — 7 exons

Exon	Start	End
ENSE00002794354	42798861	42799236
ENSE00002966229	42809365	42811587
ENSE00003461384	42804225	42804396
ENSE00003558775	42807768	42807864
ENSE00003582019	42806674	42806818
ENSE00003606769	42805722	42805884
ENSE00003666352	42803620	42803695

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 92.88.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1041 / max 41.9509, expressed in 21 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160995	0.0575	18
160996	0.0140	4
160997	0.0108	3
160998	0.0092	3
160999	0.0072	3
208201	0.0055	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	92.88	gold quality
right testis	UBERON:0004534	92.63	gold quality
testis	UBERON:0000473	89.80	gold quality
sperm	CL:0000019	87.58	gold quality
bronchial epithelial cell	CL:0002328	86.06	gold quality
bronchus	UBERON:0002185	84.20	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.86	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.19	gold quality
kidney epithelium	UBERON:0004819	76.45	gold quality
body of stomach	UBERON:0001161	75.71	gold quality
adult organism	UBERON:0007023	75.36	gold quality
epithelial cell of pancreas	CL:0000083	75.08	gold quality
mucosa of transverse colon	UBERON:0004991	74.86	gold quality
right uterine tube	UBERON:0001302	73.64	gold quality
stomach	UBERON:0000945	72.62	gold quality
rectum	UBERON:0001052	72.37	gold quality
metanephros cortex	UBERON:0010533	71.73	gold quality
transverse colon	UBERON:0001157	71.07	gold quality
lower esophagus mucosa	UBERON:0035834	71.05	gold quality
small intestine Peyer’s patch	UBERON:0003454	70.40	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	70.18	gold quality
spleen	UBERON:0002106	69.60	gold quality
body of pancreas	UBERON:0001150	69.50	gold quality
mucosa of stomach	UBERON:0001199	69.31	gold quality
granulocyte	CL:0000094	69.17	gold quality
mucosa of paranasal sinus	UBERON:0005030	69.16	silver quality
sural nerve	UBERON:0015488	68.39	gold quality
lower esophagus muscularis layer	UBERON:0035833	68.32	gold quality
lower esophagus	UBERON:0013473	68.30	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	68.28	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-86618	no	90.31
E-ANND-3	no	3.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

123 targeting CNTD1, 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-7110-3P	100.00	73.18	2486
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-590-3P	99.96	74.34	6478
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-651-3P	99.94	73.48	5177
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cntd1	ENSMUSG00000078653
caenorhabditis_elegans		WBGENE00022172

Protein

Protein identifiers

Cyclin N-terminal domain-containing protein 1 — Q8N815 (reviewed: Q8N815)

All UniProt accessions (5): B4DXR6, Q8N815, K7ELB6, K7EQE2, K7ERX8

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the different steps of crossover formation during meiotic recombination. Participates in the crossover differentiation step of crossover-specific recombination intermediates through its interaction with PRR19. In addition, stimulates crossover formation through the interactions with RFC3 and RFC4 and simultaneously regulates cell-cycle progression through interactions with CDC34 and subsequent ubiquitination of WEE1. May also participates in an active deselection process that destabilizes or removes excess pre-CO intermediates.

Subunit / interactions. Interacts with PRR19; this interaction promotes crossover formation. Interacts with RFC3 and RFC4; these interactions facilitate crossover formation. Interacts with CDC34; this interaction regulates the cell-cycle progression.

Subcellular location. Nucleus. Cytoplasm. Chromosome.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N815-1	1	yes
Q8N815-2	2

RefSeq proteins (2): NP_001317151, NP_775749* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006671	Cyclin_N	Domain
IPR036915	Cyclin-like_sf	Homologous_superfamily

Pfam: PF00134

UniProt features (5 total): chain 1, domain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N815-F1	84.94	0.62

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 132 (showing top): RACCACAR_AML_Q6, GOBP_MALE_GAMETE_GENERATION, GOBP_REGULATION_OF_MEIOTIC_CELL_CYCLE, CAGCTG_AP4_Q5, GOBP_ORGANELLE_FISSION, RGTTAMWNATT_HNF1_01, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_REPRODUCTIVE_PROCESS, TGANTCA_AP1_C, HNF1_C, TGGNNNNNNKCCAR_UNKNOWN, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, PTF1BETA_Q6

GO Biological Process (4): reciprocal meiotic recombination (GO:0007131), spermatogenesis (GO:0007283), regulation of meiotic cell cycle (GO:0051445), meiotic cell cycle (GO:0051321)

GO Molecular Function (0):

GO Cellular Component (4): nucleus (GO:0005634), chromosome (GO:0005694), cytoplasm (GO:0005737), site of double-strand break (GO:0035861)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
meiosis I	1
reciprocal homologous recombination	1
meiotic cell cycle process	1
developmental process involved in reproduction	1
male gamete generation	1
meiotic cell cycle	1
regulation of cell cycle	1
regulation of reproductive process	1
cell cycle	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1
site of DNA damage	1

Protein interactions and networks

STRING

488 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CNTD1	RNF212	Q495C1	833
CNTD1	SPO11	Q9Y5K1	762
CNTD1	MSH5	O43196	750
CNTD1	UNC119	Q13432	741
CNTD1	MSH4	O15457	707
CNTD1	SUN1	O94901	626
CNTD1	PPIE	Q9UNP9	620
CNTD1	CCNB1IP1	Q9NPC3	606
CNTD1	RAD51	Q06609	565
CNTD1	MUS81	Q96NY9	490
CNTD1	PRR19	A6NJB7	477
CNTD1	PLK2	Q9NYY3	471
CNTD1	RTEL1	Q9NZ71	445
CNTD1	HORMAD1	Q86X24	440
CNTD1	SLX1A	Q9BQ83	437

IntAct

0 interactions, top by confidence:

BioGRID (4): CNTD1 (Reconstituted Complex), CNTD1 (Affinity Capture-MS), CNTD1 (Affinity Capture-MS), SYNPO2L (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A5PK16, O08918, O42575, O96020, P24385, P24864, P25322, P30279, P30280, P30282, P39948, P39949, P39950, P41002, P47794, P48961, P49706, P49707, P50755, P50756, P51944, P51945, P51959, P53782, P55169, Q04827, Q0P5D3, Q16589, Q2KI22, Q32NJ2, Q32NM1, Q52QT8, Q5E9I1, Q5E9K7, Q5R5D0, Q5R6J5, Q5SRT8, Q5T5M9, Q5XGG5, Q61457

Diamond homologs: Q8N815, Q9D995

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1219 predictions. Top by Δscore:

Variant	Effect	Δscore
17:42799182:GCA:G	donor_gain	1.0000
17:42805810:TTTTG:T	donor_gain	1.0000
17:42805877:GGTTT:G	donor_gain	1.0000
17:42810924:CCATC:C	acceptor_gain	1.0000
17:42810925:CATC:C	acceptor_gain	1.0000
17:42810925:CATCC:C	acceptor_gain	1.0000
17:42810926:ATCC:A	acceptor_loss	1.0000
17:42810927:TC:T	acceptor_gain	1.0000
17:42810927:TCCTG:T	acceptor_loss	1.0000
17:42810928:CC:C	acceptor_gain	1.0000
17:42810929:C:CC	acceptor_gain	1.0000
17:42810929:C:CG	acceptor_loss	1.0000
17:42810930:T:A	acceptor_loss	1.0000
17:42810935:A:AC	acceptor_gain	1.0000
17:42799179:C:T	donor_gain	0.9900
17:42799185:G:GG	donor_gain	0.9900
17:42799190:G:GT	donor_gain	0.9900
17:42799191:G:T	donor_gain	0.9900
17:42799220:G:GT	donor_gain	0.9900
17:42799229:GATC:G	donor_gain	0.9900
17:42804397:G:GG	donor_gain	0.9900
17:42805719:CA:C	acceptor_loss	0.9900
17:42805720:A:AG	acceptor_gain	0.9900
17:42805720:A:T	acceptor_loss	0.9900
17:42805721:G:GC	acceptor_loss	0.9900
17:42805721:G:GG	acceptor_gain	0.9900
17:42805721:GAT:G	acceptor_gain	0.9900
17:42805721:GATA:G	acceptor_gain	0.9900
17:42805814:G:GT	donor_gain	0.9900
17:42805854:GCA:G	donor_gain	0.9900

AlphaMissense

2138 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:42807829:A:C	S263R	0.991
17:42807831:T:A	S263R	0.991
17:42807831:T:G	S263R	0.991
17:42803676:G:C	A76P	0.987
17:42804226:T:C	F83L	0.987
17:42804228:T:A	F83L	0.987
17:42804228:T:G	F83L	0.987
17:42805827:T:C	F175L	0.982
17:42805829:C:A	F175L	0.982
17:42805829:C:G	F175L	0.982
17:42804358:T:C	C127R	0.978
17:42805797:T:C	S165P	0.978
17:42804360:T:G	C127W	0.977
17:42804362:T:A	V128D	0.975
17:42806720:C:G	C209W	0.975
17:42805801:A:T	E166V	0.974
17:42807814:G:A	G258R	0.974
17:42807814:G:C	G258R	0.974
17:42804378:A:C	K133N	0.973
17:42804378:A:T	K133N	0.973
17:42807809:C:A	A256E	0.973
17:42807793:G:C	D251H	0.972
17:42804359:G:A	C127Y	0.968
17:42806718:T:C	C209R	0.968
17:42804373:A:C	S132R	0.967
17:42804375:C:A	S132R	0.967
17:42804375:C:G	S132R	0.967
17:42805804:T:C	L167P	0.966
17:42804371:C:A	A131D	0.965
17:42805810:T:A	V169D	0.965

dbSNP variants (sampled 300 via entrez): RS1000182241 (17:42808610 C>T), RS1000388767 (17:42800324 T>C), RS1000402486 (17:42808960 G>A), RS1000508480 (17:42807143 C>T), RS1000665020 (17:42799680 A>T), RS1000728431 (17:42807295 G>A), RS1001127334 (17:42798636 C>G,T), RS1001332053 (17:42803762 A>G), RS1001342277 (17:42802505 C>T), RS1001403750 (17:42803253 C>T), RS1001792122 (17:42802796 T>C), RS1002139851 (17:42804246 G>A), RS1002333185 (17:42801229 C>T), RS1002953265 (17:42797281 C>A,T), RS1003039782 (17:42805253 A>G)

Disease associations

OMIM: gene MIM:618166 | 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
GCST004125_13	Type 2 diabetes (age of onset)	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Allergens	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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