CCDC27

Summary

CCDC27 (coiled-coil domain containing 27, HGNC:26546) is a protein-coding gene on chromosome 1p36.32, encoding Coiled-coil domain-containing protein 27 (Q2M243).

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 143 total
• MANE Select transcript: NM_152492

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26546
Approved symbol	CCDC27
Name	coiled-coil domain containing 27
Location	1p36.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32825
Ensembl gene	ENSG00000162592
Ensembl biotype	protein_coding
Entrez	148870

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000294600, ENST00000462521, ENST00000636250

RefSeq mRNA: 1 — MANE Select: NM_152492 NM_152492

CCDS: CCDS50

Canonical transcript exons

ENST00000294600 — 12 exons

Exon	Start	End
ENSE00001066627	3752450	3752799
ENSE00001066629	3756733	3756890
ENSE00001066632	3754118	3754241
ENSE00001066633	3755457	3755567
ENSE00001066637	3763108	3763474
ENSE00003240679	3771401	3771645
ENSE00003482332	3767233	3767445
ENSE00003498577	3763706	3763836
ENSE00003512945	3762620	3762712
ENSE00003520105	3761281	3761430
ENSE00003567575	3769783	3769887
ENSE00003675549	3766535	3766612

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 84.12.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0974 / max 118.1843, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
324	0.0899	3
323	0.0075	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	84.12	gold quality
right testis	UBERON:0004534	83.99	gold quality
testis	UBERON:0000473	80.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.30	gold quality
buccal mucosa cell	CL:0002336	76.89	silver quality
sperm	CL:0000019	70.73	gold quality
cerebellar vermis	UBERON:0004720	66.55	gold quality
amniotic fluid	UBERON:0000173	63.16	gold quality
parotid gland	UBERON:0001831	61.58	gold quality
myocardium	UBERON:0002349	61.28	gold quality
quadriceps femoris	UBERON:0001377	60.82	gold quality
tendon of biceps brachii	UBERON:0008188	60.80	gold quality
vastus lateralis	UBERON:0001379	60.01	gold quality
gingival epithelium	UBERON:0001949	58.17	gold quality
medial globus pallidus	UBERON:0002477	58.08	gold quality
cartilage tissue	UBERON:0002418	57.85	gold quality
pericardium	UBERON:0002407	57.75	gold quality
secondary oocyte	CL:0000655	57.61	gold quality
nasal cavity epithelium	UBERON:0005384	57.35	gold quality
globus pallidus	UBERON:0001875	57.07	gold quality
trabecular bone tissue	UBERON:0002483	56.58	gold quality
decidua	UBERON:0002450	56.53	gold quality
esophagus squamous epithelium	UBERON:0006920	56.05	gold quality
oocyte	CL:0000023	55.94	gold quality
deltoid	UBERON:0001476	55.62	gold quality
Brodmann (1909) area 46	UBERON:0006483	55.56	gold quality
saphenous vein	UBERON:0007318	55.47	gold quality
seminal vesicle	UBERON:0000998	55.29	gold quality
heart right ventricle	UBERON:0002080	55.12	gold quality
cardia of stomach	UBERON:0001162	54.79	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.60
E-MTAB-6058	no	27.85
E-GEOD-70580	no	9.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting CCDC27, 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-92A-2-5P	99.75	67.01	2164
HSA-MIR-3196	98.96	63.91	326
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-629-5P	98.78	68.72	1032
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-3180	98.46	64.68	348
HSA-MIR-3180-3P	98.46	64.68	348
HSA-MIR-6816-5P	98.46	64.35	364
HSA-MIR-193B-5P	97.91	65.88	837

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc27	ENSMUSG00000039492
rattus_norvegicus	Ccdc27	ENSRNOG00000056358

Paralogs (1): FHAD1 (ENSG00000142621)

Protein

Protein identifiers

Coiled-coil domain-containing protein 27 — Q2M243 (reviewed: Q2M243)

All UniProt accessions (2): Q2M243, J3QKX2

RefSeq proteins (1): NP_689705* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR052642	CC-FHA_domain	Family

UniProt features (14 total): sequence variant 4, region of interest 3, compositionally biased region 3, sequence conflict 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2M243-F1	66.70	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chr1p36, MIKKELSEN_IPS_ICP_WITH_H3K27ME3, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_2H_DN, GSE7348_LPS_VS_TOLERIZED_AND_LPS_STIM_MACROPHAGE_DN, GSE27291_6H_VS_7D_STIM_GAMMADELTA_TCELL_DN

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

356 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC27	C10orf120	Q5SQS8	644
CCDC27	C5orf47	Q569G3	604
CCDC27	TRIM35	Q9UPQ4	582
CCDC27	C1orf174	Q8IYL3	575
CCDC27	TRIP11	Q15643	558
CCDC27	SAXO1	Q8IYX7	539
CCDC27	TP73	O15350	532
CCDC27	KCTD10	Q9H3F6	523
CCDC27	LRRC47	Q8N1G4	520
CCDC27	BLZF1	Q9H2G9	516
CCDC27	LYPD4	Q6UWN0	482
CCDC27	CEP104	O60308	481
CCDC27	TRIM42	Q8IWZ5	477
CCDC27	MEGF6	O75095	452
CCDC27	CBY2	Q8NA61	447

IntAct

7 interactions, top by confidence:

A	B	Type	Score
MAGEA11	CCDC27	psi-mi:“MI:0915”(physical association)	0.560
CCDC27	ALOX12B	psi-mi:“MI:0914”(association)	0.530
CCDC27	PLEC	psi-mi:“MI:0915”(physical association)	0.400
CCDC27	MAGEA11	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (20): CCDC27 (Two-hybrid), CLTCL1 (Affinity Capture-MS), ALOXE3 (Affinity Capture-MS), HAL (Affinity Capture-MS), ALOX12B (Affinity Capture-MS), WASF2 (Affinity Capture-MS), CCDC27 (Affinity Capture-MS), MAGEA11 (Two-hybrid), CCDC27 (Proximity Label-MS), CLTCL1 (Affinity Capture-MS), ALOX12B (Affinity Capture-MS), HAL (Affinity Capture-MS), ALOXE3 (Affinity Capture-MS), CCDC27 (Affinity Capture-MS), CC2D1B (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1L8GUX5, A0A1L8GXY6, A0A1W2P884, A2AIW0, A2AM05, A2CE83, A6PWD2, E7F5E1, O60296, P27628, P28290, P60853, Q0VF96, Q28GJ0, Q2KJD6, Q2M243, Q2MJV9, Q3V036, Q4KLH6, Q5R9L2, Q5RHB5, Q5SZL2, Q5U2Y9, Q5U3Z6, Q5U4W1, Q6AW69, Q6DIS8, Q6NRK1, Q6NRX3, Q6P2H3, Q6PCQ0, Q6ZQ06, Q70YC5, Q804T6, Q80ST9, Q86VQ0, Q8BMK0, Q8C115, Q8CFC9, Q8CGZ2

Diamond homologs: Q2M243, Q3V036

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	119
Likely benign	16
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2387 predictions. Top by Δscore:

Variant	Effect	Δscore
1:3752793:G:GT	donor_gain	1.0000
1:3752796:GACG:G	donor_gain	1.0000
1:3754107:C:CA	acceptor_gain	1.0000
1:3754117:GA:G	acceptor_gain	1.0000
1:3754239:GTG:G	donor_gain	1.0000
1:3755573:G:GT	donor_gain	1.0000
1:3756731:AG:A	acceptor_gain	1.0000
1:3756732:GG:G	acceptor_gain	1.0000
1:3756888:AAG:A	donor_loss	1.0000
1:3756889:AGGTA:A	donor_loss	1.0000
1:3756890:GGT:G	donor_loss	1.0000
1:3756891:G:GA	donor_loss	1.0000
1:3763852:G:GG	donor_gain	1.0000
1:3766529:TTCCA:T	acceptor_loss	1.0000
1:3766531:CCAG:C	acceptor_loss	1.0000
1:3766532:CA:C	acceptor_loss	1.0000
1:3766533:A:AG	acceptor_gain	1.0000
1:3766533:A:C	acceptor_loss	1.0000
1:3766534:G:GC	acceptor_gain	1.0000
1:3766534:GTT:G	acceptor_gain	1.0000
1:3767220:C:A	acceptor_gain	1.0000
1:3767221:G:A	acceptor_gain	1.0000
1:3767224:T:A	acceptor_gain	1.0000
1:3767228:CCCA:C	acceptor_loss	1.0000
1:3767229:CCA:C	acceptor_loss	1.0000
1:3767230:CA:C	acceptor_loss	1.0000
1:3767231:A:AG	acceptor_gain	1.0000
1:3767232:G:GA	acceptor_gain	1.0000
1:3767232:GC:G	acceptor_gain	1.0000
1:3767232:GCA:G	acceptor_gain	1.0000

AlphaMissense

4328 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:3769813:G:C	A592P	0.987
1:3766535:T:C	F485L	0.984
1:3766537:C:A	F485L	0.984
1:3766537:C:G	F485L	0.984
1:3769883:T:C	L615P	0.978
1:3771438:T:C	L629P	0.974
1:3763805:G:C	R474P	0.972
1:3769819:T:C	F594L	0.970
1:3769821:T:A	F594L	0.970
1:3769821:T:G	F594L	0.970
1:3769784:T:C	L582P	0.968
1:3769793:T:C	L585S	0.959
1:3766536:T:C	F485S	0.957
1:3767426:T:C	L575P	0.955
1:3769797:G:C	R586S	0.952
1:3769797:G:T	R586S	0.952
1:3763468:G:C	A439P	0.948
1:3763796:T:C	L471P	0.947
1:3769879:G:C	A614P	0.946
1:3769861:G:C	D608H	0.944
1:3763817:T:C	L478P	0.943
1:3763827:G:A	M481I	0.943
1:3763827:G:C	M481I	0.943
1:3763827:G:T	M481I	0.943
1:3769805:T:G	I589S	0.943
1:3771418:A:C	R622S	0.941
1:3771418:A:T	R622S	0.941
1:3763822:G:C	A480P	0.940
1:3769874:T:C	L612P	0.938
1:3767309:T:C	L536P	0.934

dbSNP variants (sampled 300 via entrez): RS1000228293 (1:3768207 C>A), RS1000488296 (1:3758931 C>T), RS1000539512 (1:3767958 C>T), RS1000546859 (1:3754134 C>A,T), RS1000863397 (1:3759861 T>A,C), RS1000890412 (1:3760151 T>C), RS1000914587 (1:3759253 T>C), RS1000921664 (1:3763961 T>A,C), RS1000957425 (1:3755265 G>A,C), RS1001063316 (1:3765035 C>A), RS1001072502 (1:3755457 G>A,T), RS1001074497 (1:3771965 C>A), RS1001242119 (1:3762900 C>T), RS1001422461 (1:3768588 C>G), RS1001441421 (1:3768756 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

8 associations (top):

Study	Trait	p-value
GCST001524_16	Visceral adipose tissue/subcutaneous adipose tissue ratio	2.000000e-06
GCST001525_13	Visceral fat	2.000000e-06
GCST001525_2	Visceral fat	2.000000e-06
GCST001762_852	Obesity-related traits	3.000000e-06
GCST002041_1	Blood trace element (Cu levels)	5.000000e-10
GCST004615_78	Hemoglobin concentration	2.000000e-14
GCST006804_117	Red cell distribution width	2.000000e-16
GCST90002383_142	Hematocrit	9.000000e-10

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004767	visceral:subcutaneous adipose tissue ratio
EFO:0003940	physical activity
EFO:0005267	serum copper measurement
EFO:0004509	hemoglobin measurement
EFO:0009188	Red cell distribution width
EFO:0004348	hematocrit

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
Benzo(a)pyrene	affects methylation	2
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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