CCDC85A

Summary

CCDC85A (coiled-coil domain containing 85A, HGNC:29400) is a protein-coding gene on chromosome 2p16.1, encoding Coiled-coil domain-containing protein 85A (Q96PX6). May play a role in cell-cell adhesion and epithelium development through its interaction with proteins of the beta-catenin family.

Located in adherens junction.

Source: NCBI Gene 114800 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 117 total
• MANE Select transcript: NM_001080433

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29400
Approved symbol	CCDC85A
Name	coiled-coil domain containing 85A
Location	2p16.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1912
Ensembl gene	ENSG00000055813
Ensembl biotype	protein_coding
Entrez	114800

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000407595, ENST00000894230, ENST00000894231, ENST00000894232, ENST00000963878, ENST00000963879, ENST00000963880, ENST00000963881

RefSeq mRNA: 6 — MANE Select: NM_001080433 NM_001080433, NM_001348512, NM_001348513, NM_001348514, NM_001348515, NM_001348516

CCDS: CCDS46290

Canonical transcript exons

ENST00000407595 — 6 exons

Exon	Start	End
ENSE00000407331	56192477	56193440
ENSE00001070560	56342879	56342955
ENSE00001070563	56372344	56372478
ENSE00001070565	56375816	56375935
ENSE00001266018	56183990	56184900
ENSE00001564036	56384266	56386172

Expression profiles

Bgee: expression breadth ubiquitous, 147 present calls, max score 84.01.

FANTOM5 (CAGE): breadth broad, TPM avg 3.2332 / max 58.9589, expressed in 723 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20364	1.3918	543
20362	1.1460	495
20365	0.3180	203
20363	0.2825	130
20361	0.0949	52

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	84.01	gold quality
cardiac muscle of right atrium	UBERON:0003379	79.66	gold quality
myocardium	UBERON:0002349	79.65	gold quality
left ventricle myocardium	UBERON:0006566	79.56	gold quality
upper arm skin	UBERON:0004263	79.15	gold quality
nasal cavity epithelium	UBERON:0005384	78.16	gold quality
cortical plate	UBERON:0005343	78.01	gold quality
buccal mucosa cell	CL:0002336	77.69	gold quality
frontal cortex	UBERON:0001870	76.72	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	76.10	silver quality
tendon of biceps brachii	UBERON:0008188	75.82	silver quality
kidney epithelium	UBERON:0004819	75.66	gold quality
neocortex	UBERON:0001950	75.65	gold quality
Brodmann (1909) area 9	UBERON:0013540	75.54	gold quality
anterior cingulate cortex	UBERON:0009835	75.46	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	75.39	gold quality
pancreatic ductal cell	CL:0002079	75.12	silver quality
parotid gland	UBERON:0001831	73.91	gold quality
biceps brachii	UBERON:0001507	73.77	silver quality
vastus lateralis	UBERON:0001379	73.69	gold quality
tendon	UBERON:0000043	72.85	gold quality
cerebral cortex	UBERON:0000956	72.79	gold quality
superficial temporal artery	UBERON:0001614	72.61	gold quality
apex of heart	UBERON:0002098	72.14	gold quality
calcaneal tendon	UBERON:0003701	71.90	gold quality
heart right ventricle	UBERON:0002080	71.30	gold quality
Brodmann (1909) area 46	UBERON:0006483	71.27	gold quality
right lung	UBERON:0002167	71.11	gold quality
right frontal lobe	UBERON:0002810	71.07	gold quality
omental fat pad	UBERON:0010414	70.77	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

98 targeting CCDC85A, 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-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-576-5P	99.84	70.46	2582

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc85al	ENSDARG00000005343
danio_rerio	ccdc85a	ENSDARG00000039497
mus_musculus	Ccdc85a	ENSMUSG00000032878
rattus_norvegicus	Ccdc85a	ENSRNOG00000003374
caenorhabditis_elegans		WBGENE00017931

Paralogs (2): CCDC85B (ENSG00000175602), CCDC85C (ENSG00000205476)

Protein

Protein identifiers

Coiled-coil domain-containing protein 85A — Q96PX6 (reviewed: Q96PX6)

All UniProt accessions (1): Q96PX6

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cell-cell adhesion and epithelium development through its interaction with proteins of the beta-catenin family.

Subunit / interactions. May interact with ARVCF; CTNND1; CTNND2 and PKP4.

Subcellular location. Cell junction. Adherens junction.

Similarity. Belongs to the CCDC85 family.

RefSeq proteins (6): NP_001073902, NP_001335441, NP_001335442, NP_001335443, NP_001335444, NP_001335445 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019359	CCDC85	Family

Pfam: PF10226

UniProt features (17 total): compositionally biased region 7, region of interest 4, coiled-coil region 3, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PX6-F1	60.16	0.25

Functional residue map

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

Post-translational modifications (1): 541

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): ZHAN_MULTIPLE_MYELOMA_HP_UP, GARY_CD5_TARGETS_DN, GOCC_CELL_CELL_JUNCTION, GOCC_ANCHORING_JUNCTION, COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN, MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, FIGUEROA_AML_METHYLATION_CLUSTER_7_UP, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, SKIL_TARGET_GENES, MIR8485, MIR335_3P, MIR3529_3P, MIR144_3P, MIR561_3P

GO Biological Process (0):

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

GO Cellular Component (2): adherens junction (GO:0005912), anchoring junction (GO:0070161)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cell-cell junction	1
cell junction	1

Protein interactions and networks

STRING

758 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC85A	ARHGAP23	Q9P227	576
CCDC85A	ARHGAP21	Q5T5U3	491
CCDC85A	CARD19	Q96LW7	480
CCDC85A	OR4N5	Q8IXE1	442
CCDC85A	OR4K14	Q8NGD5	412
CCDC85A	CCDC85C	A6NKD9	398
CCDC85A	INAFM2	P0DMQ5	398
CCDC85A	SANBR	Q6NSI8	390
CCDC85A	ZNF622	Q969S3	386
CCDC85A	DTD2	Q96FN9	385
CCDC85A	LY6H	O94772	385
CCDC85A	BUD13	Q9BRD0	375
CCDC85A	DOCK4	Q8N1I0	371
CCDC85A	UNC5CL	Q8IV45	370
CCDC85A	NUP43	Q8NFH3	350

IntAct

14 interactions, top by confidence:

A	B	Type	Score
TP53BP2	CCDC85A	psi-mi:“MI:0915”(physical association)	0.600
SYTL5	CCDC85A	psi-mi:“MI:0915”(physical association)	0.560
CCDC85A	NEK2	psi-mi:“MI:0915”(physical association)	0.550
PFDN1	CCDC85A	psi-mi:“MI:0915”(physical association)	0.370
CCDC85A	STMN2	psi-mi:“MI:0915”(physical association)	0.370
CCDC85A	CIBAR1	psi-mi:“MI:0914”(association)	0.350
POU3F1	DUSP3	psi-mi:“MI:0914”(association)	0.350
CCDC85A	TP53BP2	psi-mi:“MI:0915”(physical association)	0.000
SYTL5	CCDC85A	psi-mi:“MI:0915”(physical association)	0.000
VPS26C	CCDC85A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (67): TP53BP2 (Two-hybrid), SYTL5 (Two-hybrid), CCDC85A (Proximity Label-MS), JPH1 (Affinity Capture-MS), CCDC85A (Affinity Capture-MS), RABGEF1 (Affinity Capture-MS), RAB11FIP5 (Affinity Capture-MS), PPP1R13B (Affinity Capture-MS), MAP7D3 (Affinity Capture-MS), PARD3 (Affinity Capture-MS), TNKS (Affinity Capture-MS), RNF20 (Affinity Capture-MS), CCDC85C (Affinity Capture-MS), PDDC1 (Affinity Capture-MS), RBM14-RBM4 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I3QA39, A2A6T1, A2A9T0, A2AHG0, A4FUG8, A5PKL7, A6NKD9, A7MCY6, D3ZD05, E1BEQ5, E1U8D0, E9Q6B2, F1MRK3, G3V735, O14529, O15049, O60299, O75145, O94964, P60469, P70298, Q15742, Q1LZH7, Q3LUD3, Q3LUD4, Q5JTD0, Q5RCR6, Q61127, Q63ZY3, Q6DG50, Q6DIS8, Q6PDH0, Q86UU1, Q86X02, Q8BX02, Q8C7U1, Q8IZD0, Q8K1Q4, Q8K371, Q91YU6

Diamond homologs: A2CEM9, A6NKD9, E9Q6B2, H2KYP0, Q0P485, Q0V989, Q15834, Q4V872, Q5SP85, Q6DHL7, Q6PDY0, Q96PX6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	100
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2369 predictions. Top by Δscore:

Variant	Effect	Δscore
2:56184901:GT:G	donor_loss	1.0000
2:56184902:T:G	donor_loss	1.0000
2:56192472:TTCA:T	acceptor_loss	1.0000
2:56192475:A:AG	acceptor_gain	1.0000
2:56192475:AG:A	acceptor_gain	1.0000
2:56192475:AGG:A	acceptor_loss	1.0000
2:56192476:G:GG	acceptor_gain	1.0000
2:56192476:GG:G	acceptor_gain	1.0000
2:56192476:GGAT:G	acceptor_gain	1.0000
2:56379844:GCAAT:G	donor_gain	1.0000
2:56379849:G:GG	donor_gain	1.0000
2:56184901:G:GG	donor_gain	0.9900
2:56192476:GGA:G	acceptor_gain	0.9900
2:56192476:GGATA:G	acceptor_gain	0.9900
2:56193449:G:GG	donor_gain	0.9900
2:56326177:GT:G	donor_gain	0.9900
2:56326178:TT:T	donor_gain	0.9900
2:56337285:G:GT	donor_gain	0.9900
2:56373656:G:GT	donor_gain	0.9900
2:56375813:AAG:A	acceptor_gain	0.9900
2:56375997:AGTCT:A	donor_gain	0.9900
2:56379739:A:AG	acceptor_gain	0.9900
2:56379740:A:G	acceptor_gain	0.9900
2:56379742:A:AG	acceptor_gain	0.9900
2:56379743:A:G	acceptor_gain	0.9900
2:56384264:A:G	acceptor_gain	0.9900
2:56384265:GGTT:G	acceptor_gain	0.9900
2:56192474:CAGGA:C	acceptor_gain	0.9800
2:56192475:AGGA:A	acceptor_gain	0.9800
2:56259194:TGGG:T	donor_gain	0.9800

AlphaMissense

3628 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:56184779:T:C	L52P	1.000
2:56184791:T:C	L56P	1.000
2:56184842:T:C	L73P	1.000
2:56184860:G:C	R79P	1.000
2:56184866:T:C	L81P	1.000
2:56184874:C:G	H84D	1.000
2:56184878:T:C	L85P	1.000
2:56184887:T:C	I88T	1.000
2:56184887:T:G	I88S	1.000
2:56184896:T:A	L91H	1.000
2:56184896:T:C	L91P	1.000
2:56192493:T:C	L98P	1.000
2:56192501:G:C	D101H	1.000
2:56192514:T:A	L105Q	1.000
2:56192514:T:C	L105P	1.000
2:56192517:G:T	R106M	1.000
2:56192523:T:C	L108P	1.000
2:56192525:T:C	C109R	1.000
2:56192526:G:A	C109Y	1.000
2:56192527:C:G	C109W	1.000
2:56192531:T:C	F111L	1.000
2:56192532:T:C	F111S	1.000
2:56192532:T:G	F111C	1.000
2:56192533:C:A	F111L	1.000
2:56192533:C:G	F111L	1.000
2:56192535:T:A	L112Q	1.000
2:56192535:T:C	L112P	1.000
2:56192538:A:T	D113V	1.000
2:56192547:G:C	R116P	1.000
2:56192576:T:A	W126R	1.000

dbSNP variants (sampled 300 via entrez): RS1000000455 (2:56342560 C>T), RS1000004028 (2:56209026 G>A), RS1000027581 (2:56201300 A>G), RS1000037018 (2:56274169 C>G,T), RS1000053161 (2:56345872 T>A), RS1000069348 (2:56303291 G>A), RS1000084478 (2:56282522 A>G), RS1000093020 (2:56286732 A>G,T), RS1000094260 (2:56379034 T>A), RS1000105128 (2:56345536 C>T), RS1000113909 (2:56268293 C>A), RS1000152297 (2:56191905 G>T), RS1000163977 (2:56354308 C>G,T), RS1000168628 (2:56384150 T>G), RS1000178689 (2:56204644 A>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

8 associations (top):

Study	Trait	p-value
GCST000880_12	Menarche (age at onset)	1.000000e-10
GCST002541_37	Menarche (age at onset)	6.000000e-28
GCST002938_26	Copper levels	4.000000e-06
GCST003400_13	Type 2 diabetes	7.000000e-10
GCST003400_51	Type 2 diabetes	5.000000e-06
GCST005352_13	Paclitaxel disposition in epithelial ovarian cancer	6.000000e-06
GCST007831_9	Anti-thyroglobulin (TgAb) levels in Hashimoto’s thyroiditis	9.000000e-06
GCST010396_283	Gut microbiota (bacterial taxa, hurdle binary method)	7.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Dexamethasone	affects cotreatment, increases expression	2
Valproic Acid	increases expression, affects expression	2
bisphenol F	affects cotreatment, increases expression	1
bisphenol A	affects cotreatment, increases expression	1
trichostatin A	increases expression	1
o,p’-DDT	increases methylation	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
benzo(e)pyrene	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, affects response to substance, increases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
Resveratrol	decreases expression, affects cotreatment	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Calcitriol	increases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	increases methylation	1
Formaldehyde	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lead	affects expression	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Methapyrilene	decreases methylation	1
Nickel	decreases expression	1

Clinical trials (associated diseases)

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