CCDC169

Summary

CCDC169 (coiled-coil domain containing 169, HGNC:34361) is a protein-coding gene on chromosome 13q13.3, encoding Coiled-coil domain-containing protein 169 (A6NNP5).

At a glance

• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_001144981

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34361
Approved symbol	CCDC169
Name	coiled-coil domain containing 169
Location	13q13.3
Locus type	gene with protein product
Status	Approved
Aliases	RP11-251J8.1, LOC728591
Ensembl gene	ENSG00000242715
Ensembl biotype	protein_coding
Entrez	728591

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 7 protein_coding, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000239859, ENST00000239860, ENST00000379862, ENST00000379864, ENST00000471781, ENST00000477250, ENST00000479850, ENST00000485600, ENST00000486683, ENST00000491049, ENST00000503173, ENST00000506800, ENST00000510088

RefSeq mRNA: 7 — MANE Select: NM_001144981 NM_001144981, NM_001144982, NM_001144983, NM_001144984, NM_001144985, NM_001144986, NM_001198908

CCDS: CCDS45027, CCDS45028, CCDS45029, CCDS53863, CCDS55897

Canonical transcript exons

ENST00000239859 — 8 exons

Exon	Start	End
ENSE00002053198	36230775	36231292
ENSE00003458592	36283469	36283509
ENSE00003461130	36297637	36297814
ENSE00003530362	36253803	36253856
ENSE00003535421	36283592	36283702
ENSE00003558291	36248606	36248682
ENSE00003607804	36254045	36254143
ENSE00003620145	36295778	36295857

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 99.09.

FANTOM5 (CAGE): breadth broad, TPM avg 2.9433 / max 137.5809, expressed in 859 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136777	2.9433	859

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.09	gold quality
left testis	UBERON:0004533	96.54	gold quality
right testis	UBERON:0004534	96.34	gold quality
testis	UBERON:0000473	93.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.08	gold quality
cortical plate	UBERON:0005343	75.47	gold quality
adult organism	UBERON:0007023	75.11	gold quality
stromal cell of endometrium	CL:0002255	73.05	gold quality
smooth muscle tissue	UBERON:0001135	69.76	gold quality
endothelial cell	CL:0000115	68.33	gold quality
adrenal tissue	UBERON:0018303	66.31	gold quality
muscle layer of sigmoid colon	UBERON:0035805	65.46	gold quality
prefrontal cortex	UBERON:0000451	63.39	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	63.27	gold quality
hindlimb stylopod muscle	UBERON:0004252	62.52	gold quality
left adrenal gland	UBERON:0001234	62.19	gold quality
urinary bladder	UBERON:0001255	62.11	gold quality
right adrenal gland	UBERON:0001233	61.65	gold quality
cerebellar vermis	UBERON:0004720	61.58	gold quality
right adrenal gland cortex	UBERON:0035827	61.36	gold quality
adrenal gland	UBERON:0002369	60.83	gold quality
left adrenal gland cortex	UBERON:0035825	60.61	gold quality
cauda epididymis	UBERON:0004360	59.87	gold quality
nucleus accumbens	UBERON:0001882	59.62	gold quality
mucosa of paranasal sinus	UBERON:0005030	59.49	gold quality
anterior cingulate cortex	UBERON:0009835	59.46	gold quality
prostate gland	UBERON:0002367	59.39	gold quality
adrenal cortex	UBERON:0001235	59.33	gold quality
lower lobe of lung	UBERON:0008949	59.29	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	31.46
E-ANND-3	yes	4.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting CCDC169, 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-656-3P	100.00	72.15	2788
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-548AU-3P	99.70	68.22	1373
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-6513-3P	99.59	69.77	1102
HSA-MIR-1273H-3P	99.29	67.55	980
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-4744	99.01	69.91	1581
HSA-MIR-12135	98.99	70.26	1814
HSA-MIR-138-2-3P	98.91	68.33	1643

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc169	ENSMUSG00000048655
rattus_norvegicus	Ccdc169	ENSRNOG00000038095

Protein

Protein identifiers

Coiled-coil domain-containing protein 169 — A6NNP5 (reviewed: A6NNP5)

All UniProt accessions (2): A6NNP5, E9PBZ7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CCDC169 family.

Isoforms (6)

UniProt ID	Names	Canonical?
A6NNP5-1	1	yes
A6NNP5-2	2
A6NNP5-3	3
A6NNP5-4	4
A6NNP5-5	5
A6NNP5-6	6

RefSeq proteins (7): NP_001138453, NP_001138454, NP_001138455, NP_001138456, NP_001138457, NP_001138458, NP_001185837 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028022	DUF4600	Family

Pfam: PF15372

UniProt features (11 total): splice variant 6, chain 1, region of interest 1, sequence variant 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NNP5-F1	80.59	0.52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): GOZGIT_ESR1_TARGETS_DN, chr13q13, FOSTER_KDM1A_TARGETS_UP, ZNF10_TARGET_GENES, ZNF213_TARGET_GENES, ZNF423_TARGET_GENES, MIR3688_3P, MIR656_3P, MIR4694_3P, MIR670_5P, MIR345_3P, MIR12120, MIR5197_5P, MIR6852_5P, MIR603

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

242 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC169	TMEM161B	Q8NDZ6	510
CCDC169	CCDC190	Q86UF4	479
CCDC169	CCDC74B	Q96LY2	476
CCDC169	PROSER1	Q86XN7	475
CCDC169	MAB21L1	Q13394	471
CCDC169	SOHLH2	Q9NX45	464
CCDC169	STPG2	Q8N412	447
CCDC169	CCDC125	Q86Z20	435
CCDC169	ZNF287	Q9HBT7	430
CCDC169	ZNF641	Q96N77	429
CCDC169	CENATAC	Q86UT8	424
CCDC169	MAGEB16	A2A368	419
CCDC169	KLHDC9	Q8NEP7	414
CCDC169	SPART	Q8N0X7	411
CCDC169	NBEA	Q8NFP9	403

IntAct

0 interactions, top by confidence:

BioGRID (3): CCDC169 (Synthetic Lethality), CCDC169 (Cross-Linking-MS (XL-MS)), CCDC169 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1ZB42, A3LYF7, A6NNP5, A6ZML8, B7ZD04, C3KJF2, C5E000, O02197, O13786, O13964, P22468, P47149, P86347, Q03615, Q03818, Q09858, Q12343, Q177A7, Q23523, Q290F0, Q3SYZ9, Q561Q8, Q561X3, Q59U73, Q5M8Y7, Q5XG48, Q60MF5, Q621Z7, Q68F53, Q6C5P0, Q6CJA3, Q6CMB6, Q6CMK9, Q6CRY0, Q6CVN3, Q6FNK3, Q6FQ75, Q6FS55, Q75EX7, Q7PLI2

Diamond homologs: A6NNP5, Q3KPT0, Q8BXX9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1811 predictions. Top by Δscore:

Variant	Effect	Δscore
13:36231180:T:TA	donor_gain	1.0000
13:36248599:GACTT:G	donor_loss	1.0000
13:36248600:ACTTA:A	donor_loss	1.0000
13:36248601:CTT:C	donor_loss	1.0000
13:36248601:CTTA:C	donor_loss	1.0000
13:36248602:T:TC	donor_loss	1.0000
13:36248603:T:TG	donor_loss	1.0000
13:36248603:TACGT:T	donor_loss	1.0000
13:36248604:A:AC	donor_gain	1.0000
13:36248604:A:C	donor_loss	1.0000
13:36248605:C:CC	donor_gain	1.0000
13:36248605:C:G	donor_loss	1.0000
13:36248605:CG:C	donor_gain	1.0000
13:36253798:GTTAC:G	donor_loss	1.0000
13:36253799:TTAC:T	donor_loss	1.0000
13:36253799:TTACC:T	donor_loss	1.0000
13:36253800:TA:T	donor_loss	1.0000
13:36253801:A:C	donor_loss	1.0000
13:36253801:ACC:A	donor_loss	1.0000
13:36253802:C:G	donor_loss	1.0000
13:36253802:CCTG:C	donor_loss	1.0000
13:36276012:AAAAC:A	donor_gain	1.0000
13:36283586:TTGTA:T	donor_loss	1.0000
13:36283587:TGTA:T	donor_loss	1.0000
13:36283588:GTAC:G	donor_loss	1.0000
13:36283589:TA:T	donor_loss	1.0000
13:36283590:A:AG	donor_loss	1.0000
13:36283591:CCT:C	donor_loss	1.0000
13:36295768:A:AC	donor_gain	1.0000
13:36295769:C:CC	donor_gain	1.0000

AlphaMissense

1399 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:36283694:A:G	W58R	0.947
13:36283694:A:T	W58R	0.947
13:36283692:C:A	W58C	0.892
13:36283692:C:G	W58C	0.892
13:36283651:A:G	L72P	0.880
13:36254124:A:G	L112P	0.875
13:36295828:A:G	L38P	0.874
13:36283669:A:G	L66P	0.860
13:36283630:A:G	L79P	0.855
13:36254115:A:G	L115P	0.849
13:36283476:A:G	M103T	0.820
13:36283671:T:A	Q65H	0.801
13:36283671:T:G	Q65H	0.801
13:36295807:A:G	L45P	0.799
13:36283642:T:G	Q75P	0.794
13:36283684:C:G	R61P	0.791
13:36297658:A:G	L21S	0.789
13:36253831:C:G	R147P	0.782
13:36283693:C:G	W58S	0.782
13:36283689:T:A	K59N	0.761
13:36283689:T:G	K59N	0.761
13:36283682:A:C	Y62D	0.759
13:36283475:C:A	M103I	0.758
13:36283475:C:G	M103I	0.758
13:36283475:C:T	M103I	0.758
13:36254085:T:G	Q125P	0.753
13:36254136:A:G	L108S	0.742
13:36283659:A:C	N69K	0.739
13:36283659:A:T	N69K	0.739
13:36254094:A:G	L122P	0.731

dbSNP variants (sampled 300 via entrez): RS1000034709 (13:36256715 G>A), RS1000039585 (13:36298659 A>C), RS1000066311 (13:36294868 T>A,C,G), RS1000078128 (13:36244225 G>T), RS1000116850 (13:36294639 C>A,T), RS1000149179 (13:36281343 C>A), RS1000165326 (13:36229204 G>A,C), RS1000220416 (13:36295515 T>C), RS1000239346 (13:36278621 G>C), RS1000257822 (13:36286405 A>C), RS1000366999 (13:36240688 T>C), RS1000392247 (13:36298954 G>A), RS1000420001 (13:36287729 C>T), RS1000492735 (13:36260273 TG>T), RS1000514550 (13:36280871 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	decreases expression, increases expression, affects cotreatment	4
Valproic Acid	increases expression	2
propionaldehyde	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	decreases expression	1
aflatoxin B2	decreases methylation	1
nickel sulfate	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Rotenone	increases expression	1
Tretinoin	decreases expression	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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