CCDC121

Summary

CCDC121 (coiled-coil domain containing 121, HGNC:25833) is a protein-coding gene on chromosome 2p23.3, encoding Coiled-coil domain-containing protein 121 (Q6ZUS5).

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_024584

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25833
Approved symbol	CCDC121
Name	coiled-coil domain containing 121
Location	2p23.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ43364, FLJ13646
Ensembl gene	ENSG00000176714
Ensembl biotype	protein_coding
Entrez	79635

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000324364, ENST00000394775, ENST00000522876, ENST00000866112, ENST00000947586

RefSeq mRNA: 2 — MANE Select: NM_024584 NM_001142683, NM_024584

CCDS: CCDS1759, CCDS46247

Canonical transcript exons

ENST00000324364 — 2 exons

Exon	Start	End
ENSE00001285744	27625638	27627917
ENSE00001375708	27628950	27629012

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 89.89.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5957 / max 86.1217, expressed in 726 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
27519	1.5335	700
27518	0.0622	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	89.89	gold quality
right testis	UBERON:0004534	86.04	gold quality
left testis	UBERON:0004533	85.87	gold quality
oocyte	CL:0000023	85.17	gold quality
testis	UBERON:0000473	84.64	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.55	gold quality
sperm	CL:0000019	84.37	silver quality
male germ cell	CL:0000015	81.47	silver quality
calcaneal tendon	UBERON:0003701	81.41	gold quality
hair follicle	UBERON:0002073	79.01	gold quality
ventricular zone	UBERON:0003053	78.59	gold quality
ganglionic eminence	UBERON:0004023	75.77	gold quality
islet of Langerhans	UBERON:0000006	75.71	gold quality
right uterine tube	UBERON:0001302	75.10	gold quality
hindlimb stylopod muscle	UBERON:0004252	74.40	gold quality
mucosa of paranasal sinus	UBERON:0005030	73.71	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	73.61	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.01	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.93	gold quality
descending thoracic aorta	UBERON:0002345	72.61	gold quality
choroid plexus epithelium	UBERON:0003911	72.19	silver quality
germinal epithelium of ovary	UBERON:0001304	71.66	gold quality
rectum	UBERON:0001052	71.37	gold quality
ovary	UBERON:0000992	70.95	gold quality
muscle of leg	UBERON:0001383	70.90	gold quality
heart left ventricle	UBERON:0002084	70.75	gold quality
spinal cord	UBERON:0002240	70.72	gold quality
smooth muscle tissue	UBERON:0001135	70.69	gold quality
thoracic aorta	UBERON:0001515	70.69	gold quality
ascending aorta	UBERON:0001496	70.35	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

60 targeting CCDC121, 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-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-21-5P	99.46	70.54	1035
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-5582-5P	99.27	71.42	1879
HSA-MIR-590-5P	99.25	70.76	930
HSA-MIR-3152-3P	99.10	66.35	678

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Coiled-coil domain-containing protein 121 — Q6ZUS5 (reviewed: Q6ZUS5)

All UniProt accessions (2): Q6ZUS5, E5RHR4

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZUS5-1	1	yes
Q6ZUS5-2	2

RefSeq proteins (2): NP_001136155, NP_078860* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032777	DUF4515	Domain

Pfam: PF14988

UniProt features (5 total): coiled-coil region 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZUS5-F1	87.88	0.74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): MODULE_205, WCTCNATGGY_UNKNOWN, LASTOWSKA_COAMPLIFIED_WITH_MYCN, ZHENG_IL22_SIGNALING_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, STEIN_ESRRA_TARGETS_UP, MIKKELSEN_IPS_LCP_WITH_H3K4ME3, MIKKELSEN_ES_LCP_WITH_H3K4ME3, MARTENS_TRETINOIN_RESPONSE_DN, VERHAAK_GLIOBLASTOMA_NEURAL, PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7, KRAS.600.LUNG.BREAST_UP.V1_DN, KRAS.BREAST_UP.V1_DN, KRAS.LUNG.BREAST_UP.V1_DN, FOXN3_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

442 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC121	SPATA31H1	Q68DN1	768
CCDC121	ZNF512	Q96ME7	729
CCDC121	KRTCAP3	Q53RY4	654
CCDC121	NRBP1	Q9UHY1	617
CCDC121	GPN1	Q9HCN4	582
CCDC121	FNDC4	Q9H6D8	542
CCDC121	SLC4A1AP	Q9BWU0	515
CCDC121	IFT172	Q9UG01	503
CCDC121	GTF3C2	Q8WUA4	477
CCDC121	SUPT7L	O94864	475
CCDC121	IQUB	Q8NA54	395
CCDC121	CCDC178	Q5BJE1	394
CCDC121	BLTP3B	A0JNW5	392
CCDC121	ZNF513	Q8N8E2	382
CCDC121	ESPNL	Q6ZVH7	357

IntAct

26 interactions, top by confidence:

A	B	Type	Score
CCDC121	TFIP11	psi-mi:“MI:0915”(physical association)	0.780
NUP62	CCDC121	psi-mi:“MI:0915”(physical association)	0.670
CCDC121	RINT1	psi-mi:“MI:0915”(physical association)	0.670
RINT1	CCDC121	psi-mi:“MI:0915”(physical association)	0.670
CCDC121	NUP62	psi-mi:“MI:0915”(physical association)	0.670
USHBP1	CCDC121	psi-mi:“MI:0915”(physical association)	0.560
CCDC121	USHBP1	psi-mi:“MI:0915”(physical association)	0.560
LTBR	ZNF724	psi-mi:“MI:0914”(association)	0.530
CCDC121	SCRN1	psi-mi:“MI:0914”(association)	0.530
KDM1A	CCDC121	psi-mi:“MI:0915”(physical association)	0.370
NECAB2	CCDC121	psi-mi:“MI:0915”(physical association)	0.370
CCDC121	TFIP11	psi-mi:“MI:0915”(physical association)	0.000
TFIP11	CCDC121	psi-mi:“MI:0915”(physical association)	0.000
ezrA	CCDC121	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): CCDC121 (Two-hybrid), CCDC121 (Two-hybrid), CCDC121 (Two-hybrid), USHBP1 (Two-hybrid), TBC1D15 (Affinity Capture-MS), UBE2E3 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), CCDC121 (Affinity Capture-MS), CCDC121 (Two-hybrid), CCDC121 (Two-hybrid), CCDC121 (Two-hybrid), CCDC121 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D15 (Affinity Capture-MS), UBE2E3 (Affinity Capture-MS)

ESM2 similar proteins: A0AHI4, A1RIW7, A3D5F9, A3QD78, A4Y7M2, A5UE98, A5UHC9, A6W0E2, A6WP70, A9L4H0, B0URI2, B1WNF0, B2VDR3, B3PKX8, B7KI38, B8E944, B8F412, C1L1Y7, C6DFW6, P43987, P44796, P73956, P75395, Q0HJT8, Q0HW34, Q0I588, Q116P5, Q21K43, Q2SJL9, Q38WQ2, Q3J9J5, Q49407, Q4QMS9, Q4R6V9, Q562C6, Q5RBR4, Q65U90, Q6D4E8, Q6L8L3, Q6ZUS5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

205 predictions. Top by Δscore:

Variant	Effect	Δscore
2:27628388:A:AC	donor_gain	0.9800
2:27628389:C:CC	donor_gain	0.9800
2:27628871:T:TA	donor_gain	0.9800
2:27627915:AACCT:A	acceptor_loss	0.9700
2:27627916:ACC:A	acceptor_loss	0.9700
2:27627917:CCTGA:C	acceptor_loss	0.9700
2:27627918:CTGAA:C	acceptor_loss	0.9700
2:27627919:T:G	acceptor_loss	0.9700
2:27629002:G:GT	donor_gain	0.9600
2:27627918:C:CC	acceptor_gain	0.9400
2:27628949:CCCG:C	donor_gain	0.9400
2:27628844:T:TA	donor_gain	0.9300
2:27628954:T:A	donor_gain	0.9200
2:27628964:CG:C	donor_gain	0.9200
2:27628329:T:A	donor_gain	0.9100
2:27628829:AGCTC:A	donor_gain	0.8900
2:27628897:ATCAG:A	donor_gain	0.8900
2:27628958:TTCTG:T	donor_gain	0.8900
2:27627913:CAAAC:C	acceptor_gain	0.8800
2:27628833:C:CA	donor_gain	0.8700
2:27629002:G:T	donor_gain	0.8700
2:27628898:T:C	donor_gain	0.8600
2:27628962:G:T	donor_gain	0.8300
2:27628414:T:TA	donor_gain	0.8200
2:27627914:AAAC:A	acceptor_gain	0.8100
2:27627915:AAC:A	acceptor_gain	0.8100
2:27627916:AC:A	acceptor_gain	0.8100
2:27627917:CC:C	acceptor_gain	0.8100
2:27628529:C:CA	donor_gain	0.7900
2:27628872:C:A	donor_gain	0.7900

AlphaMissense

1813 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:27627672:A:G	L43P	0.801
2:27627111:A:G	L230P	0.796
2:27627449:C:A	Q117H	0.796
2:27627449:C:G	Q117H	0.796
2:27627250:C:G	A184P	0.794
2:27627531:A:G	L90P	0.789
2:27627769:C:G	A11P	0.789
2:27627626:C:A	W58C	0.769
2:27627626:C:G	W58C	0.769
2:27627153:A:G	L216P	0.768
2:27627174:A:G	L209P	0.753
2:27627543:A:G	L86P	0.753
2:27627163:C:G	A213P	0.751
2:27627756:C:G	R15P	0.749
2:27627696:T:A	E35V	0.737
2:27627458:C:A	K114N	0.729
2:27627458:C:G	K114N	0.729
2:27627726:A:G	L25P	0.728
2:27627628:A:G	W58R	0.716
2:27627628:A:T	W58R	0.716
2:27627736:A:G	S22P	0.706
2:27627584:T:A	R72S	0.674
2:27627584:T:G	R72S	0.674
2:27627535:C:G	A89P	0.668
2:27627450:T:G	Q117P	0.662
2:27627363:A:G	L146P	0.659
2:27627577:A:G	S75P	0.658
2:27627700:C:G	A34P	0.642
2:27627479:C:A	M107I	0.636
2:27627479:C:G	M107I	0.636

dbSNP variants (sampled 300 via entrez): RS1000493511 (2:27627509 T>C), RS1000844195 (2:27627985 C>T), RS1002890420 (2:27629610 G>C), RS1002983607 (2:27629316 G>A), RS1003053872 (2:27630064 G>A,T), RS1003329265 (2:27630237 A>G), RS1004302515 (2:27630324 A>G), RS1005129525 (2:27630278 C>G), RS1005995004 (2:27629306 T>C), RS1006132112 (2:27629100 G>A,C,T), RS1006237492 (2:27626467 C>A), RS1006350373 (2:27625968 CA>C,CAA), RS1008672173 (2:27630739 A>G), RS1009201696 (2:27628038 C>T), RS1010197286 (2:27629603 G>A)

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

7 associations (top):

Study	Trait	p-value
GCST001006_2	Waist Circumference - Triglycerides (WC-TG)	1.000000e-09
GCST003858_1	Oral cavity cancer	4.000000e-08
GCST008103_38	Bipolar disorder	1.000000e-07
GCST008985_3	Triglycerides	7.000000e-07
GCST009391_1049	Metabolite levels	2.000000e-06
GCST009391_1335	Metabolite levels	1.000000e-06
GCST009391_1873	Metabolite levels	2.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0000195	metabolic syndrome
EFO:0004530	triglyceride measurement
EFO:0010358	lysophosphatidylcholine 16:1 measurement
EFO:0010362	lysophosphatidylcholine 20:3 measurement
EFO:0010411	triacylglycerol 50:4 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	decreases expression, affects cotreatment	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	affects expression, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
propionaldehyde	decreases expression	1
bisphenol A	affects cotreatment, increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
2-butenal	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
ferrous chloride	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases methylation	1
jinfukang	increases expression, affects cotreatment	1
Air Pollutants	decreases expression, increases abundance	1
Benztropine	increases expression	1
Calcitriol	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Cuprizone	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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