CCDC83

Summary

CCDC83 (coiled-coil domain containing 83, HGNC:28535) is a protein-coding gene on chromosome 11q14.1-q14.2, encoding Coiled-coil domain-containing protein 83 (Q8IWF9).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 78 total
• MANE Select transcript: NM_001286159

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28535
Approved symbol	CCDC83
Name	coiled-coil domain containing 83
Location	11q14.1-q14.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC34732, FLJ42119, CT148, KP-CoT-23
Ensembl gene	ENSG00000150676
Ensembl biotype	protein_coding
Entrez	220047

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000280245, ENST00000342404, ENST00000526729, ENST00000529676

RefSeq mRNA: 2 — MANE Select: NM_001286159 NM_001286159, NM_173556

CCDS: CCDS66196, CCDS8271

Canonical transcript exons

ENST00000342404 — 11 exons

Exon	Start	End
ENSE00000995878	85882513	85882675
ENSE00000995879	85886200	85886367
ENSE00000995881	85916028	85916233
ENSE00001101498	85915419	85915498
ENSE00002170566	85855383	85855584
ENSE00003466239	85895293	85895384
ENSE00003481941	85898947	85899015
ENSE00003564395	85865096	85865218
ENSE00003580058	85911281	85911402
ENSE00003643973	85873211	85873295
ENSE00003903383	85919349	85920013

Expression profiles

Bgee: expression breadth broad, 46 present calls, max score 98.30.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0258 / max 23.4564, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116093	0.0258	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.30	gold quality
left testis	UBERON:0004533	86.17	gold quality
right testis	UBERON:0004534	85.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.15	gold quality
testis	UBERON:0000473	84.15	gold quality
adult organism	UBERON:0007023	66.77	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	64.21	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
epithelial cell of pancreas	CL:0000083	53.70	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
tibialis anterior	UBERON:0001385	53.20	silver quality
pancreatic ductal cell	CL:0002079	52.14	silver quality
myocardium	UBERON:0002349	50.25	gold quality
deltoid	UBERON:0001476	49.96	gold quality
ileal mucosa	UBERON:0000331	49.19	silver quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.62	gold quality
granulocyte	CL:0000094	46.14	silver quality
vastus lateralis	UBERON:0001379	45.40	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
lower lobe of lung	UBERON:0008949	43.01	silver quality
secondary oocyte	CL:0000655	42.57	gold quality
oviduct epithelium	UBERON:0004804	42.10	silver quality
skeletal muscle tissue	UBERON:0001134	41.74	gold quality
muscle tissue	UBERON:0002385	41.73	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting CCDC83, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-4524A-5P	99.57	71.73	1193
HSA-MIR-4524B-5P	99.57	71.68	1195
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-5587-5P	99.07	68.58	838
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-511-5P	98.97	70.94	2268
HSA-MIR-138-2-3P	98.91	68.33	1643
HSA-MIR-29B-1-5P	98.86	68.35	1364

Literature-anchored findings (GeneRIF, showing 2)

• HSD-9 is specific in human testes, and the expression pattern of its encoding product is similar to those of some endocytosis proteins. (PMID:17633455)
• These data suggest that KP-CoT-23 is a novel CT antigen that may be useful for the diagnosis and immunotherapy of cancer. (PMID:22923163)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc83	ENSDARG00000077179
mus_musculus	Ccdc83	ENSMUSG00000030617
rattus_norvegicus	Ccdc83	ENSRNOG00000052220

Protein

Protein identifiers

Coiled-coil domain-containing protein 83 — Q8IWF9 (reviewed: Q8IWF9)

All UniProt accessions (2): Q8IWF9, H0YDV3

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IWF9-1	1	yes
Q8IWF9-2	2
Q8IWF9-3	3

RefSeq proteins (2): NP_001273088, NP_775827 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026702	CCDC83	Family

UniProt features (11 total): splice variant 4, coiled-coil region 2, chain 1, region of interest 1, sequence conflict 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IWF9-F1	73.76	0.47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): GOZGIT_ESR1_TARGETS_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, WANG_LMO4_TARGETS_DN, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, DACH1_TARGET_GENES, HES2_TARGET_GENES, ZNF512_TARGET_GENES, ZNF563_TARGET_GENES, ZNF592_TARGET_GENES, MIR6867_5P, MIR4729, MIR15A_5P

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

204 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC83	IQCF1	Q8N6M8	623
CCDC83	CDADC1	Q9BWV3	583
CCDC83	DRC9	Q9H095	549
CCDC83	SPAG9	O60271	539
CCDC83	RPH3AL	Q9UNE2	510
CCDC83	FMR1NB	Q8N0W7	507
CCDC83	KLHL10	Q6JEL2	466
CCDC83	EIF4ENIF1	Q9NRA8	448
CCDC83	DMRTC2	Q8IXT2	441
CCDC83	FSCN3	Q9NQT6	426
CCDC83	PACRG	Q96M98	409
CCDC83	ARID4A	P29374	398
CCDC83	AAGAB	Q6PD74	396
CCDC83	RBM46	Q8TBY0	395
CCDC83	CCDC110	Q8TBZ0	392

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CCDC83	FAM161B	psi-mi:“MI:0915”(physical association)	0.560
CCDC83	MCC	psi-mi:“MI:0914”(association)	0.350
FAM161B	CCDC83	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): MCC (Affinity Capture-MS), RBM12 (Affinity Capture-MS), CHMP2A (Affinity Capture-MS), KLC1 (Affinity Capture-MS), PPID (Affinity Capture-MS), TTC33 (Affinity Capture-MS), ASPM (Affinity Capture-MS), CCDC83 (Synthetic Lethality), FAM161B (Two-hybrid), PPID (Affinity Capture-MS), MCC (Affinity Capture-MS), RBM12 (Affinity Capture-MS), CCDC50 (Affinity Capture-MS), CCDC83 (Cross-Linking-MS (XL-MS)), CCDC83 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GVH7, A6PVS8, A8DZJ1, A9Q751, D3ZSP7, D4AEC2, Q08AD1, Q08CX2, Q14DL3, Q2T9P0, Q2TA00, Q32KQ1, Q3UZ57, Q3V0J4, Q4G0U5, Q4R7B1, Q4R7Z7, Q5S003, Q5SUV2, Q5T1B0, Q5ZLS8, Q63164, Q66HC0, Q69CM7, Q6AXP3, Q6AYL8, Q6IRN6, Q6NXP0, Q6Q759, Q80X60, Q86WZ0, Q8C1B1, Q8C4J0, Q8C636, Q8CDN1, Q8CDU5, Q8IWF9, Q8N7B9, Q8N7U6, Q8ND61

Diamond homologs: Q2TA00, Q8IWF9, Q95K40, Q9D4V3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	65
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2279 predictions. Top by Δscore:

Variant	Effect	Δscore
11:85865219:G:GG	donor_gain	1.0000
11:85873205:TCTCA:T	acceptor_loss	1.0000
11:85873206:CTCA:C	acceptor_loss	1.0000
11:85873208:CAG:C	acceptor_loss	1.0000
11:85873209:A:AG	acceptor_gain	1.0000
11:85873209:AG:A	acceptor_loss	1.0000
11:85873210:G:GC	acceptor_loss	1.0000
11:85873210:G:GG	acceptor_gain	1.0000
11:85873210:GAT:G	acceptor_gain	1.0000
11:85873292:AAGA:A	donor_gain	1.0000
11:85873293:AGA:A	donor_gain	1.0000
11:85873294:GA:G	donor_gain	1.0000
11:85873294:GAG:G	donor_gain	1.0000
11:85873295:AG:A	donor_loss	1.0000
11:85873296:G:GG	donor_gain	1.0000
11:85873297:TG:T	donor_loss	1.0000
11:85873298:GAGT:G	donor_loss	1.0000
11:85873299:A:AC	donor_loss	1.0000
11:85873300:G:C	donor_loss	1.0000
11:85882641:G:GT	donor_gain	1.0000
11:85882641:G:T	donor_gain	1.0000
11:85882660:G:GT	donor_gain	1.0000
11:85882661:A:T	donor_gain	1.0000
11:85895289:A:AG	acceptor_gain	1.0000
11:85895290:A:G	acceptor_gain	1.0000
11:85895291:A:G	acceptor_gain	1.0000
11:85915414:TTTA:T	acceptor_loss	1.0000
11:85915415:TTA:T	acceptor_loss	1.0000
11:85915416:TAG:T	acceptor_loss	1.0000
11:85915417:A:AG	acceptor_gain	1.0000

AlphaMissense

2790 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:85882624:G:C	A98P	0.984
11:85886352:G:C	A166P	0.980
11:85886301:G:C	A149P	0.978
11:85899005:T:C	L221P	0.978
11:85882556:T:C	L75P	0.971
11:85895376:G:C	A199P	0.968
11:85898950:G:C	A203P	0.967
11:85886274:T:C	Y140H	0.962
11:85886275:A:C	Y140S	0.962
11:85882639:T:A	W103R	0.959
11:85882639:T:C	W103R	0.959
11:85886248:T:C	L131P	0.955
11:85886223:G:C	A123P	0.950
11:85886364:T:C	S170P	0.944
11:85895311:T:C	L177P	0.942
11:85911333:T:C	L242P	0.942
11:85886274:T:G	Y140D	0.940
11:85882523:T:C	L64S	0.938
11:85886279:G:C	K141N	0.934
11:85886279:G:T	K141N	0.934
11:85911354:T:C	L249P	0.934
11:85873264:T:C	L50P	0.933
11:85886265:T:A	W137R	0.932
11:85886265:T:C	W137R	0.932
11:85882616:T:A	V95D	0.931
11:85911366:T:C	L253P	0.931
11:85886341:T:A	V162D	0.929
11:85882641:G:C	W103C	0.927
11:85882641:G:T	W103C	0.927
11:85911346:T:A	N246K	0.923

dbSNP variants (sampled 300 via entrez): RS1000044917 (11:85882097 G>A), RS1000059529 (11:85899085 A>G), RS1000091733 (11:85899444 C>T), RS1000126186 (11:85863736 T>A,C,G), RS1000205648 (11:85855093 T>G), RS1000273509 (11:85861029 G>A), RS1000295433 (11:85905819 A>T), RS1000321087 (11:85900798 C>T), RS1000337426 (11:85901004 G>A,T), RS1000385423 (11:85857233 C>T), RS1000465426 (11:85867933 C>A), RS1000465928 (11:85906011 A>G), RS1000497051 (11:85897579 T>C), RS1000532675 (11:85855714 G>A,T), RS1000582152 (11:85907557 C>T)

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

1 associations (top):

Study	Trait	p-value
GCST003461_1	IgG response to Plasmodium falciparum antigens (GLURP, MSP2 FC27, MSP2 3D7)	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007812	Plasmodium falciparum antigen IgG measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects methylation, increases methylation	2
FR900359	decreases phosphorylation	1
bisphenol A	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Estradiol	decreases expression, decreases reaction	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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