CCDC54

Summary

CCDC54 (coiled-coil domain containing 54, HGNC:30703) is a protein-coding gene on chromosome 3q13.12, encoding Coiled-coil domain-containing protein 54 (Q8NEL0).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_032600

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30703
Approved symbol	CCDC54
Name	coiled-coil domain containing 54
Location	3q13.12
Locus type	gene with protein product
Status	Approved
Aliases	NYD-SP17, FLJ25362, SP17
Ensembl gene	ENSG00000138483
Ensembl biotype	protein_coding
Entrez	84692

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000261058

RefSeq mRNA: 1 — MANE Select: NM_032600 NM_032600

CCDS: CCDS2949

Canonical transcript exons

ENST00000261058 — 1 exons

Exon	Start	End
ENSE00000934129	107377439	107378635

Expression profiles

Bgee: expression breadth broad, 98 present calls, max score 98.60.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1163 / max 113.6002, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
37781	0.0616	3
37782	0.0547	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.60	gold quality
left testis	UBERON:0004533	97.44	gold quality
right testis	UBERON:0004534	97.27	gold quality
testis	UBERON:0000473	94.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.56	gold quality
adult organism	UBERON:0007023	83.95	gold quality
tibialis anterior	UBERON:0001385	63.60	silver quality
ileal mucosa	UBERON:0000331	59.73	silver quality
stromal cell of endometrium	CL:0002255	55.19	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
deltoid	UBERON:0001476	53.78	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
epithelial cell of pancreas	CL:0000083	53.07	gold quality
heart left ventricle	UBERON:0002084	51.59	gold quality
cardiac ventricle	UBERON:0002082	51.20	gold quality
myocardium	UBERON:0002349	50.25	gold quality
corpus callosum	UBERON:0002336	48.98	silver quality
apex of heart	UBERON:0002098	47.79	gold quality
placenta	UBERON:0001987	47.34	gold quality
quadriceps femoris	UBERON:0001377	47.29	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
pancreatic ductal cell	CL:0002079	46.97	silver quality
lower esophagus mucosa	UBERON:0035834	46.09	silver quality
heart	UBERON:0000948	45.53	gold quality
right adrenal gland cortex	UBERON:0035827	45.52	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality
left ovary	UBERON:0002119	44.78	gold quality
adrenal tissue	UBERON:0018303	44.60	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.80

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• data supporting the rationale for further investigations of Sp17 for tumor vaccines in testicular cancer. (review) (PMID:16138340)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc54	ENSMUSG00000050685
rattus_norvegicus	Ccdc54	ENSRNOG00000028005

Protein

Protein identifiers

Coiled-coil domain-containing protein 54 — Q8NEL0 (reviewed: Q8NEL0)

Alternative names: Testis development protein NYD-SP17

All UniProt accessions (2): A0A140VJF9, Q8NEL0

RefSeq proteins (1): NP_115989* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037758	CCDC54	Family

UniProt features (4 total): chain 1, coiled-coil region 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEL0-F1	59.69	0.20

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): 182

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): TGACATY_UNKNOWN, YKACATTT_UNKNOWN, MARTENS_TRETINOIN_RESPONSE_DN, GSE14026_TH1_VS_TH17_DN, GSE14308_TH1_VS_NAIVE_CD4_TCELL_DN, chr3q13, GSE27786_ERYTHROBLAST_VS_MONO_MAC_UP, GSE36392_EOSINOPHIL_VS_MAC_IL25_TREATED_LUNG_UP, GSE9037_WT_VS_IRAK4_KO_LPS_1H_STIM_BMDM_UP, GSE2770_IL12_VS_TGFB_AND_IL12_TREATED_ACT_CD4_TCELL_2H_UP, GSE1566_WT_VS_EZH2_KO_LN_TCELL_UP, GSE22601_IMMATURE_CD4_SINGLE_POSITIVE_VS_DOUBLE_POSITIVE_THYMOCYTE_UP, GSE2585_CTEC_VS_THYMIC_DC_UP, ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP, GSE4590_PRE_BCELL_VS_SMALL_PRE_BCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

354 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC54	C22orf23	Q9BZE7	592
CCDC54	CCDC187	A0A096LP49	543
CCDC54	TMCO2	Q7Z6W1	543
CCDC54	ADAM29	Q9UKF5	537
CCDC54	GARIN1B	Q96KD3	515
CCDC54	RIMBP3	Q9UFD9	513
CCDC54	CXorf65	A6NEN9	507
CCDC54	C20orf173	Q96LM9	507
CCDC54	FAM209A	Q5JX71	503
CCDC54	SOX30	O94993	485
CCDC54	TNP1	P09430	484
CCDC54	FAM81B	Q96LP2	484
CCDC54	ZC3H11D	Q8NA57	480
CCDC54	CIMIP4	O43247	476
CCDC54	BBX	Q8WY36	471

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CCDC54	RSL1D1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): CCDC54 (Proximity Label-MS), CCDC54 (Negative Genetic)

ESM2 similar proteins: A0A023PXJ3, A1STV0, A5HBD7, A6NC05, A6X970, A8Y985, C1P605, F5HA06, O06472, O94339, P03080, P03081, P03083, P04009, P0C306, P0C307, P0DOI8, P0DOI9, P0DOJ0, P21071, P21972, P24598, P24756, P24852, P39551, Q01009, Q01031, Q03418, Q04406, Q07509, Q09264, Q0V9U8, Q11177, Q32759, Q3E8K6, Q4R363, Q5T3Y7, Q5UPF3, Q66H70, Q6ENI8

Diamond homologs: Q29RU3, Q4R363, Q8NEL0, Q9DAL3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

191 predictions. Top by Δscore:

Variant	Effect	Δscore
3:107377990:GCAT:G	donor_gain	0.6600
3:107378065:G:GT	donor_gain	0.6000
3:107378181:GCCC:G	donor_gain	0.5700
3:107378358:A:T	donor_gain	0.5500
3:107377973:T:TA	acceptor_gain	0.5400
3:107378018:A:T	donor_gain	0.5400
3:107378187:T:G	donor_gain	0.5200
3:107378072:GGG:G	donor_gain	0.5000
3:107378073:GGG:G	donor_gain	0.5000
3:107378152:G:GT	donor_gain	0.5000
3:107378176:A:T	donor_gain	0.4900
3:107378153:A:T	donor_gain	0.4800
3:107377991:C:T	donor_gain	0.4700
3:107378259:C:G	donor_gain	0.4700
3:107378354:G:GT	donor_gain	0.4700
3:107377866:A:AG	acceptor_gain	0.4500
3:107377867:G:GG	acceptor_gain	0.4500
3:107378291:C:T	donor_gain	0.4500
3:107378258:A:AG	donor_gain	0.4400
3:107378076:TA:T	donor_gain	0.4200
3:107378077:AA:A	donor_gain	0.4200
3:107378078:AA:A	donor_gain	0.4200
3:107378254:C:G	donor_gain	0.4200
3:107378357:G:GT	donor_gain	0.4200
3:107378338:C:G	donor_gain	0.4100
3:107378389:T:G	donor_gain	0.4100
3:107378175:G:GT	donor_gain	0.4000
3:107378250:GAAAC:G	donor_gain	0.4000
3:107377865:AAGTC:A	acceptor_gain	0.3900
3:107377866:AGTC:A	acceptor_gain	0.3900

AlphaMissense

2185 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:107378329:T:A	W248R	0.947
3:107378329:T:C	W248R	0.947
3:107378344:T:C	F253L	0.914
3:107378346:T:A	F253L	0.914
3:107378346:T:G	F253L	0.914
3:107378398:T:C	F271L	0.887
3:107378400:C:A	F271L	0.887
3:107378400:C:G	F271L	0.887
3:107378362:T:A	W259R	0.879
3:107378362:T:C	W259R	0.879
3:107378339:T:C	L251P	0.863
3:107378368:T:C	F261L	0.863
3:107378370:T:A	F261L	0.863
3:107378370:T:G	F261L	0.863
3:107377826:T:C	L80P	0.860
3:107378411:T:C	L275P	0.860
3:107378371:T:C	F262L	0.838
3:107378373:C:A	F262L	0.838
3:107378373:C:G	F262L	0.838
3:107378364:G:C	W259C	0.834
3:107378364:G:T	W259C	0.834
3:107378506:T:C	C307R	0.834
3:107378407:T:A	W274R	0.826
3:107378407:T:C	W274R	0.826
3:107378331:G:C	W248C	0.818
3:107378331:G:T	W248C	0.818
3:107378339:T:A	L251Q	0.786
3:107378319:C:A	D244E	0.778
3:107378319:C:G	D244E	0.778
3:107378337:G:C	K250N	0.778

dbSNP variants (sampled 300 via entrez): RS1001944039 (3:107378858 A>T), RS1002985467 (3:107375872 A>G), RS1004668893 (3:107377330 A>C), RS1006173824 (3:107375481 T>G), RS1006341931 (3:107378689 A>C,G), RS1007578771 (3:107375474 T>C), RS1007807388 (3:107376317 CAA>C,CA), RS1007896540 (3:107378638 T>C), RS1008852169 (3:107376956 A>G,T), RS1009022536 (3:107377811 C>G,T), RS1009317573 (3:107377263 G>A), RS1011983071 (3:107377621 G>A,T), RS1013411055 (3:107376229 G>A,C), RS1014812146 (3:107375863 C>G), RS1016892766 (3:107377382 T>G)

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

4 associations (top):

Study	Trait	p-value
GCST008170_7	Thyroglobulin plasma levels	4.000000e-06
GCST009391_1522	Metabolite levels	5.000000e-06
GCST009391_368	Metabolite levels	7.000000e-06
GCST010796_118	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0010050	thyroglobulin measurement
EFO:0010418	triacylglycerol 52:6 measurement
EFO:0010435	triacylglycerol 56:8 measurement
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
hydroxyhydroquinone	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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