CCDC30

Summary

CCDC30 (coiled-coil domain containing 30, HGNC:26103) is a protein-coding gene on chromosome 1p34.2, encoding Coiled-coil domain-containing protein 30 (Q5VVM6).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 352 total — 2 pathogenic, 3 likely-pathogenic
• MANE Select transcript: NM_001395517

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26103
Approved symbol	CCDC30
Name	coiled-coil domain containing 30
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20972, PFD6L, LOC728621
Ensembl gene	ENSG00000186409
Ensembl biotype	protein_coding
Entrez	728621

Gene structure

Transcript identifiers

Ensembl transcripts: 56 — 22 protein_coding, 13 protein_coding_CDS_not_defined, 12 nonsense_mediated_decay, 9 retained_intron

ENST00000340612, ENST00000342022, ENST00000462063, ENST00000468651, ENST00000471390, ENST00000471699, ENST00000475614, ENST00000477155, ENST00000492422, ENST00000495044, ENST00000507855, ENST00000509712, ENST00000514642, ENST00000653544, ENST00000653735, ENST00000654604, ENST00000654683, ENST00000655164, ENST00000655265, ENST00000655447, ENST00000655845, ENST00000656306, ENST00000656470, ENST00000657248, ENST00000657597, ENST00000658812, ENST00000660083, ENST00000660830, ENST00000660910, ENST00000660938, ENST00000661864, ENST00000663139, ENST00000663155, ENST00000663866, ENST00000664192, ENST00000664418, ENST00000664805, ENST00000665137, ENST00000665176, ENST00000665217, ENST00000665466, ENST00000665792, ENST00000665812, ENST00000666893, ENST00000667055, ENST00000667205, ENST00000667947, ENST00000668036, ENST00000668663, ENST00000669138, ENST00000669471, ENST00000670292, ENST00000670783, ENST00000670982, ENST00000671281, ENST00000671538

RefSeq mRNA: 10 — MANE Select: NM_001395517 NM_001080850, NM_001355224, NM_001355226, NM_001355227, NM_001395379, NM_001395382, NM_001395383, NM_001395384, NM_001395385, NM_001395517

CCDS: CCDS30690, CCDS90929, CCDS90931

Canonical transcript exons

ENST00000657597 — 21 exons

Exon	Start	End
ENSE00003462819	42642473	42642609
ENSE00003465826	42556156	42556405
ENSE00003468561	42610978	42611090
ENSE00003485527	42539173	42539310
ENSE00003487957	42536476	42536601
ENSE00003494500	42646135	42646317
ENSE00003503454	42545410	42545579
ENSE00003522835	42589321	42589483
ENSE00003527184	42577020	42577229
ENSE00003599985	42653376	42653443
ENSE00003628742	42637237	42637378
ENSE00003641412	42644693	42644807
ENSE00003678803	42566296	42566475
ENSE00003679144	42581360	42581514
ENSE00003821726	42498818	42498916
ENSE00003823490	42497098	42497213
ENSE00003824084	42490158	42490229
ENSE00003826110	42482663	42482816
ENSE00003855836	42480461	42480566
ENSE00003864303	42653818	42657190
ENSE00003966234	42463286	42463898

Expression profiles

Bgee: expression breadth ubiquitous, 181 present calls, max score 94.52.

FANTOM5 (CAGE): breadth broad, TPM avg 3.9999 / max 172.2434, expressed in 890 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2458	3.6550	781
2456	0.3449	163

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	94.52	gold quality
sural nerve	UBERON:0015488	89.58	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.67	gold quality
sperm	CL:0000019	86.85	silver quality
adenohypophysis	UBERON:0002196	86.84	gold quality
bronchial epithelial cell	CL:0002328	85.57	gold quality
pituitary gland	UBERON:0000007	84.74	gold quality
calcaneal tendon	UBERON:0003701	84.53	gold quality
left testis	UBERON:0004533	83.90	gold quality
male germ cell	CL:0000015	83.72	silver quality
right testis	UBERON:0004534	82.92	gold quality
left lobe of thyroid gland	UBERON:0001120	82.43	gold quality
right lobe of thyroid gland	UBERON:0001119	81.80	gold quality
epithelium of bronchus	UBERON:0002031	81.50	gold quality
testis	UBERON:0000473	81.48	gold quality
thyroid gland	UBERON:0002046	81.36	gold quality
cortical plate	UBERON:0005343	80.32	gold quality
ventricular zone	UBERON:0003053	80.25	gold quality
bronchus	UBERON:0002185	80.05	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.79	gold quality
metanephros cortex	UBERON:0010533	79.77	gold quality
buccal mucosa cell	CL:0002336	77.59	silver quality
right lung	UBERON:0002167	77.35	gold quality
left ovary	UBERON:0002119	77.25	gold quality
colonic epithelium	UBERON:0000397	76.64	gold quality
caudate nucleus	UBERON:0001873	76.44	gold quality
right frontal lobe	UBERON:0002810	76.39	gold quality
nucleus accumbens	UBERON:0001882	76.19	gold quality
anterior cingulate cortex	UBERON:0009835	75.97	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.31
E-CURD-135	no	1090.19
E-MTAB-2983	no	20.78

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• A novel human prefoldin PFD6L from the fetal brain was cloned and characterized. (PMID:16710767)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc30	ENSMUSG00000028637
rattus_norvegicus	Ccdc30	ENSRNOG00000008560

Protein

Protein identifiers

Coiled-coil domain-containing protein 30 — Q5VVM6 (reviewed: Q5VVM6)

Alternative names: Prefoldin subunit 6-like protein

All UniProt accessions (24): Q5VVM6, A0A2U3TZI4, A0A590UJ28, A0A590UJ34, A0A590UJ69, A0A590UJ77, A0A590UJ83, A0A590UJ92, A0A590UJA8, A0A590UJC1, A0A590UJC6, A0A590UJI4, A0A590UJK6, A0A590UJL6, A0A590UJL9, A0A590UJQ0, A0A590UJW7, A0A590UK05, A0A590UK19, A0A590UK35, A0A590UKA3, A0A590UKA6, D6RFH8, F6UBW0

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in brain, kidney, pancreas, placenta, liver, thymus and prostate.

Similarity. Belongs to the prefoldin subunit beta family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5VVM6-1	1	yes
Q5VVM6-2	2

RefSeq proteins (10): NP_001074319, NP_001342153, NP_001342155, NP_001342156, NP_001382308, NP_001382311, NP_001382312, NP_001382313, NP_001382314, NP_001382446* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031476	DUF4686	Family
IPR052825	CCD-Prefoldin_beta-like	Family

Pfam: PF15742

UniProt features (15 total): region of interest 4, compositionally biased region 3, coiled-coil region 3, splice variant 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VVM6-F1	70.27	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): chr1p34, DBP_Q6, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, BARX1_TARGET_GENES, FOXN3_TARGET_GENES, HOXB6_TARGET_GENES, ZSCAN31_TARGET_GENES, GSE10240_IL22_VS_IL22_AND_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, MIR6739_5P, MIR6733_5P, MIR3153, MIR4779, GSE14769_UNSTIM_VS_360MIN_LPS_BMDM_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

844 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC30	WDR64	B1ANS9	617
CCDC30	ARMH2	H3BNL8	543
CCDC30	HMGXB4	Q9UGU5	535
CCDC30	RIMKLA	Q8IXN7	527
CCDC30	ZMYND12	Q9H0C1	447
CCDC30	BRD7	Q9NPI1	423
CCDC30	CFAP144	A6NL82	419
CCDC30	C1orf50	Q9BV19	417
CCDC30	NAGPA	Q9UK23	408
CCDC30	FGFRL1	Q8N441	398
CCDC30	TMEM190	Q8WZ59	375
CCDC30	CCDC150	Q8NCX0	374
CCDC30	CCAR1	Q8IX12	371
CCDC30	ZNF497	Q6ZNH5	371
CCDC30	RERE	Q9P2R6	371

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CCDC30	CCT6A	psi-mi:“MI:0915”(physical association)	0.400
BRAP	CCDC30	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (10): CCDC30 (Two-hybrid), CCDC30 (Synthetic Lethality), CCDC30 (Proximity Label-MS), CCDC30 (Affinity Capture-MS), CCDC30 (Affinity Capture-RNA), CCDC30 (Affinity Capture-RNA), CCDC30 (Proximity Label-MS), CCDC30 (Affinity Capture-MS), EEA1 (Cross-Linking-MS (XL-MS)), CCDC30 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1W2P884, A0P8Z5, A2AM05, A2BGP7, A7E3D8, A8MT70, B0CM36, B1WC58, E9PVD1, O75410, O95447, Q1RMS0, Q2M243, Q3UPP8, Q3V036, Q4KMA0, Q4R3Q7, Q4R3X1, Q5PQS2, Q5R9L2, Q5U465, Q5U5Q9, Q5VVM6, Q5VX52, Q5XI03, Q66KC9, Q6NRH3, Q6NZK5, Q6P9F0, Q6PJW8, Q6Y685, Q70YC5, Q7Z4H7, Q86T90, Q86Z20, Q8BFU3, Q8BG89, Q8BVF4, Q8CDM4, Q8IW35

Diamond homologs: Q5VVM6, Q8BVF4, Q8WP33

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	3
Uncertain significance	202
Likely benign	113
Benign	6

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
590783	NM_024664.4(PPCS):c.538G>C (p.Ala180Pro)	Pathogenic
59966	GRCh38/hg38 1p34.2-34.1(chr1:40462415-44668040)x1	Pathogenic
1679771	NM_001287511.2(PPCS):c.636_639del (p.Leu213fs)	Likely pathogenic
242842	GRCh37/hg19 1p34.2(chr1:41343608-43121507)x1	Likely pathogenic
3767229	NM_024664.4(PPCS):c.727G>C (p.Ala243Pro)	Likely pathogenic

SpliceAI

3748 predictions. Top by Δscore:

Variant	Effect	Δscore
1:42490153:TTTA:T	acceptor_loss	1.0000
1:42490154:TTAG:T	acceptor_loss	1.0000
1:42490156:A:AG	acceptor_gain	1.0000
1:42490156:A:G	acceptor_loss	1.0000
1:42490157:G:GT	acceptor_gain	1.0000
1:42490157:GATTC:G	acceptor_gain	1.0000
1:42490229:GGT:G	donor_loss	1.0000
1:42490230:G:GG	donor_gain	1.0000
1:42490230:GT:G	donor_loss	1.0000
1:42490231:T:A	donor_loss	1.0000
1:42497090:T:TA	acceptor_gain	1.0000
1:42497096:A:AG	acceptor_gain	1.0000
1:42497096:A:AT	acceptor_loss	1.0000
1:42497096:AGAT:A	acceptor_gain	1.0000
1:42497097:G:GA	acceptor_gain	1.0000
1:42497097:GA:G	acceptor_gain	1.0000
1:42497097:GAT:G	acceptor_gain	1.0000
1:42497097:GATG:G	acceptor_gain	1.0000
1:42497097:GATGC:G	acceptor_gain	1.0000
1:42497209:AAATG:A	donor_gain	1.0000
1:42497210:AATG:A	donor_gain	1.0000
1:42497211:ATG:A	donor_gain	1.0000
1:42497212:TG:T	donor_gain	1.0000
1:42497212:TGG:T	donor_loss	1.0000
1:42497213:GG:G	donor_gain	1.0000
1:42497214:G:A	donor_loss	1.0000
1:42497214:G:GG	donor_gain	1.0000
1:42498814:TAA:T	acceptor_loss	1.0000
1:42498816:A:AT	acceptor_loss	1.0000
1:42498816:A:G	acceptor_gain	1.0000

AlphaMissense

6258 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:42637317:G:C	R526P	0.991
1:42642537:T:C	L568P	0.981
1:42642516:T:C	L561P	0.980
1:42644746:T:C	L610P	0.973
1:42577033:T:C	L290P	0.970
1:42566405:T:C	L262P	0.968
1:42566417:G:C	R266P	0.962
1:42566456:T:C	L279P	0.959
1:42581370:T:C	L359P	0.956
1:42577041:G:C	A293P	0.953
1:42577218:G:C	A352P	0.953
1:42644725:T:C	L603S	0.948
1:42611075:T:C	L494P	0.946
1:42637275:T:C	L512P	0.945
1:42539198:T:C	L48P	0.942
1:42642504:A:C	Q557P	0.941
1:42577126:T:C	L321P	0.940
1:42637359:T:C	L540P	0.938
1:42644767:T:C	L617S	0.933
1:42581459:G:C	A389P	0.931
1:42644773:G:C	R619P	0.928
1:42611042:T:C	L483P	0.925
1:42566369:G:C	R250P	0.924
1:42642500:G:C	A556P	0.919
1:42566392:G:C	A258P	0.916
1:42637293:G:C	R518P	0.915
1:42637329:T:C	I530T	0.913
1:42642558:A:C	Q575P	0.913
1:42642546:A:C	Q571P	0.909
1:42611021:T:C	L476P	0.908

dbSNP variants (sampled 300 via entrez): RS1000014577 (1:42460994 G>A,T), RS1000018078 (1:42480868 C>T), RS1000075223 (1:42489097 C>T), RS1000087683 (1:42527089 G>A), RS1000140972 (1:42479029 C>G), RS1000142128 (1:42550729 G>A,T), RS1000144769 (1:42615411 C>G), RS1000154209 (1:42620181 C>A), RS1000162877 (1:42639861 G>A), RS1000165879 (1:42620468 G>T), RS1000169802 (1:42500705 G>T), RS1000199902 (1:42568675 G>A), RS1000217144 (1:42613937 G>C,T), RS1000243232 (1:42523926 C>A), RS1000283476 (1:42468105 A>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:618189, MIM:603896

GenCC curated gene-disease

Mondo (2): cardiomyopathy, dilated, 2c (MONDO:0032592), leukoencephalopathy with vanishing white matter 1 (MONDO:0020507)

Orphanet (1): Cree leukoencephalopathy (Orphanet:99854)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST006629_47	Pulse pressure	9.000000e-16
GCST007267_179	Systolic blood pressure	2.000000e-09
GCST007269_21	Pulse pressure	6.000000e-12

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0006335	systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, decreases methylation, increases methylation	4
sodium arsenite	affects expression, increases expression	2
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, increases methylation	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
bisphenol S	affects cotreatment, increases methylation	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	increases abundance, increases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	increases expression, affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Silicon Dioxide	increases expression	1
Smoke	increases expression, increases abundance	1
Theophylline	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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