CCDC148

Summary

CCDC148 (coiled-coil domain containing 148, HGNC:25191) is a protein-coding gene on chromosome 2q24.1, encoding Coiled-coil domain-containing protein 148 (Q8NFR7).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_138803

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25191
Approved symbol	CCDC148
Name	coiled-coil domain containing 148
Location	2q24.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC125588
Ensembl gene	ENSG00000153237
Ensembl biotype	protein_coding
Entrez	130940

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 7 protein_coding, 4 nonsense_mediated_decay

ENST00000283233, ENST00000409187, ENST00000409889, ENST00000417066, ENST00000448656, ENST00000451554, ENST00000454257, ENST00000491563, ENST00000707084, ENST00000900274, ENST00000956036

RefSeq mRNA: 3 — MANE Select: NM_138803 NM_001301684, NM_001301685, NM_138803

CCDS: CCDS33304, CCDS77476

Canonical transcript exons

ENST00000283233 — 14 exons

Exon	Start	End
ENSE00001754844	158171073	158172259
ENSE00002483396	158358449	158358570
ENSE00003463775	158338726	158338907
ENSE00003479448	158456415	158456753
ENSE00003513874	158345215	158345318
ENSE00003515895	158338990	158339085
ENSE00003518884	158309433	158309639
ENSE00003565327	158340598	158340680
ENSE00003600667	158176521	158176661
ENSE00003615634	158340242	158340393
ENSE00003631018	158220595	158220713
ENSE00003639045	158250772	158250912
ENSE00003663173	158313756	158313894
ENSE00003692302	158178879	158178996

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 89.72.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	89.72	gold quality
bronchus	UBERON:0002185	87.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.90	gold quality
secondary oocyte	CL:0000655	83.84	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.56	gold quality
oocyte	CL:0000023	81.51	gold quality
buccal mucosa cell	CL:0002336	81.25	silver quality
calcaneal tendon	UBERON:0003701	78.17	gold quality
mucosa of paranasal sinus	UBERON:0005030	78.12	gold quality
caput epididymis	UBERON:0004358	77.26	gold quality
right uterine tube	UBERON:0001302	76.97	gold quality
ventricular zone	UBERON:0003053	76.10	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.84	gold quality
metanephros cortex	UBERON:0010533	72.97	gold quality
pancreatic ductal cell	CL:0002079	72.25	silver quality
adult mammalian kidney	UBERON:0000082	72.05	gold quality
corpus epididymis	UBERON:0004359	70.28	gold quality
kidney	UBERON:0002113	70.03	gold quality
medial globus pallidus	UBERON:0002477	69.77	silver quality
cortical plate	UBERON:0005343	69.68	gold quality
ganglionic eminence	UBERON:0004023	68.21	gold quality
cortex of kidney	UBERON:0001225	68.00	gold quality
testis	UBERON:0000473	67.85	gold quality
left testis	UBERON:0004533	67.58	gold quality
cauda epididymis	UBERON:0004360	66.74	gold quality
right testis	UBERON:0004534	66.62	gold quality
oviduct epithelium	UBERON:0004804	66.61	gold quality
prefrontal cortex	UBERON:0000451	66.56	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	66.55	gold quality
adenohypophysis	UBERON:0002196	66.44	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-119	yes	55.07
E-ANND-3	yes	6.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting CCDC148, 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-3646	100.00	73.56	5283
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-221-3P	99.86	71.56	1329
HSA-MIR-222-3P	99.86	71.35	1337
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4659A-3P	99.80	72.62	4248

Literature-anchored findings (GeneRIF, showing 2)

• CCCDC148 is associated with acute lung injury in mice (PMID:21297076)
• Attempted replication of pharmacogenetic association of variants in PPP1R14C and CCDC148 with aromatase inhibitor-induced musculoskeletal symptoms. (PMID:38359166)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc148	ENSMUSG00000036641
rattus_norvegicus	Ccdc148	ENSRNOG00000057740

Paralogs (1): CCDC112 (ENSG00000164221)

Protein

Protein identifiers

Coiled-coil domain-containing protein 148 — Q8NFR7 (reviewed: Q8NFR7)

All UniProt accessions (7): Q8NFR7, A0A9L9PXV0, B8ZZV3, F8WBK8, F8WC92, F8WCV9, F8WCW7

Isoforms (4)

UniProt ID	Names	Canonical?
Q8NFR7-1	1	yes
Q8NFR7-2	2
Q8NFR7-3	3
Q8NFR7-4	4

RefSeq proteins (3): NP_001288613, NP_001288614, NP_620158* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039902	CCDC148/CCDC112	Family

UniProt features (16 total): splice variant 8, coiled-coil region 3, sequence variant 3, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NFR7-F1	79.14	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): ATF_B, RNGTGGGC_UNKNOWN, LFA1_Q6, GCANCTGNY_MYOD_Q6, CREBP1_Q2, CREB_Q4, WCTCNATGGY_UNKNOWN, TGCTGAY_UNKNOWN, chr2q24, E4F1_Q6, ATF3_Q6, MYOD_Q6, IK3_01, CREBP1CJUN_01, TGGAAA_NFAT_Q4_01

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

404 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC148	LRRC49	Q8IUZ0	516
CCDC148	MORN3	Q6PF18	449
CCDC148	CCNI2	Q6ZMN8	443
CCDC148	UPP2	O95045	423
CCDC148	C11orf65	Q8NCR3	417
CCDC148	MB21D2	Q8IYB1	403
CCDC148	MTRNR2L10	P0CJ77	399
CCDC148	TDRP	Q86YL5	394
CCDC148	ZNF253	O75346	392
CCDC148	PGCKA1	Q8IY42	391
CCDC148	RASGEF1C	Q8N431	377
CCDC148	FAM135A	Q9P2D6	371
CCDC148	MGAT4C	Q9UBM8	371
CCDC148	QSER1	Q2KHR3	366
CCDC148	NAA16	Q6N069	366

IntAct

12 interactions, top by confidence:

A	B	Type	Score
SAT1	CCDC148	psi-mi:“MI:0915”(physical association)	0.700
CCDC148	SAT1	psi-mi:“MI:0915”(physical association)	0.700
CCDC148	USHBP1	psi-mi:“MI:0915”(physical association)	0.560
CBX1	KPNA3	psi-mi:“MI:0914”(association)	0.530
CCDC148	SCGB2A1	psi-mi:“MI:0914”(association)	0.350
STXBP1	CCDC148	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (25): CCDC148 (Two-hybrid), CCDC148 (Two-hybrid), SCGB1D1 (Affinity Capture-MS), LTF (Affinity Capture-MS), SCGB2A1 (Affinity Capture-MS), LACRT (Affinity Capture-MS), TEX9 (Affinity Capture-MS), IGHA1 (Affinity Capture-MS), SCGB2A1 (Affinity Capture-MS), TEX9 (Affinity Capture-MS), LTF (Affinity Capture-MS), LACRT (Affinity Capture-MS), SCGB1D1 (Affinity Capture-MS), IGHA1 (Affinity Capture-MS), CCDC148 (Two-hybrid)

ESM2 similar proteins: A0AUP1, A0JMY4, A3KQH2, D6REC4, E1C760, F1QRC1, F1RKB1, F7AEX0, Q15051, Q17QH9, Q2IA00, Q32KY1, Q3USS3, Q3V079, Q3ZC62, Q45GW3, Q4R6T7, Q4R7Y8, Q4R8R3, Q4R8Y5, Q4V8E4, Q5PQQ6, Q5XI65, Q5XIR6, Q6P0R8, Q6P5U8, Q7T0Y4, Q7Z4T9, Q80VN0, Q8BP00, Q8BRC6, Q8C6E0, Q8C9J3, Q8CDK3, Q8CDV6, Q8HZY8, Q8NA47, Q8NA54, Q8NCU4, Q8ND07

Diamond homologs: Q6P5U8, Q8HZY8, Q8NFR7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	11
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

3313 predictions. Top by Δscore:

Variant	Effect	Δscore
2:158172256:TTAT:T	acceptor_gain	1.0000
2:158178996:CCTT:C	acceptor_gain	1.0000
2:158250770:A:AC	donor_gain	1.0000
2:158250771:C:CC	donor_gain	1.0000
2:158250803:T:TA	donor_gain	1.0000
2:158250908:CGAAC:C	acceptor_gain	1.0000
2:158250910:AACCT:A	acceptor_loss	1.0000
2:158250911:AC:A	acceptor_gain	1.0000
2:158250911:ACCTG:A	acceptor_loss	1.0000
2:158250912:CC:C	acceptor_gain	1.0000
2:158250912:CCT:C	acceptor_loss	1.0000
2:158250913:C:CC	acceptor_gain	1.0000
2:158309431:A:AC	donor_gain	1.0000
2:158309432:C:CC	donor_gain	1.0000
2:158309432:C:CG	donor_loss	1.0000
2:158309638:ACC:A	acceptor_loss	1.0000
2:158309640:C:CC	acceptor_gain	1.0000
2:158309640:CTGA:C	acceptor_loss	1.0000
2:158313748:GTACT:G	donor_loss	1.0000
2:158313749:TAC:T	donor_loss	1.0000
2:158313751:CTC:C	donor_loss	1.0000
2:158313752:T:TA	donor_loss	1.0000
2:158313753:CACCA:C	donor_loss	1.0000
2:158313754:A:AC	donor_gain	1.0000
2:158313754:ACCAA:A	donor_loss	1.0000
2:158313755:C:CC	donor_gain	1.0000
2:158313891:GTTT:G	acceptor_gain	1.0000
2:158313892:TTT:T	acceptor_gain	1.0000
2:158313892:TTTC:T	acceptor_loss	1.0000
2:158313893:TT:T	acceptor_gain	1.0000

AlphaMissense

3951 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:158309537:C:G	A336P	0.971
2:158172219:C:G	R557P	0.964
2:158309443:A:G	L367P	0.963
2:158172222:A:G	L556P	0.961
2:158345249:A:G	W73R	0.957
2:158345249:A:T	W73R	0.957
2:158176548:G:C	F534L	0.950
2:158176548:G:T	F534L	0.950
2:158176550:A:G	F534L	0.950
2:158178984:T:A	R461S	0.949
2:158178984:T:G	R461S	0.949
2:158309516:C:G	A343P	0.948
2:158172242:T:A	R549S	0.946
2:158172242:T:G	R549S	0.946
2:158172214:C:G	A559P	0.939
2:158178996:C:A	R457S	0.934
2:158178996:C:G	R457S	0.934
2:158172146:T:A	R581S	0.931
2:158172146:T:G	R581S	0.931
2:158250903:A:G	W374R	0.930
2:158250903:A:T	W374R	0.930
2:158250899:C:G	R375P	0.929
2:158250872:A:G	L384P	0.928
2:158178985:C:G	R461T	0.927
2:158172207:A:G	L561P	0.926
2:158172258:A:T	I544K	0.923
2:158345227:A:G	L80P	0.918
2:158309536:G:T	A336D	0.917
2:158313839:A:C	Y274D	0.916
2:158176629:T:A	R507S	0.913

dbSNP variants (sampled 300 via entrez): RS1000002135 (2:158253124 T>C), RS1000014993 (2:158336598 A>C,G), RS1000024235 (2:158316520 A>G), RS1000033278 (2:158253317 T>C), RS1000035818 (2:158263823 T>C), RS1000055153 (2:158344925 C>G), RS1000060742 (2:158209608 C>T), RS1000067881 (2:158363258 C>T), RS1000078596 (2:158203674 C>G), RS1000088243 (2:158428612 T>C), RS1000089769 (2:158233437 T>A,C), RS1000095600 (2:158335326 A>C), RS1000098694 (2:158323393 T>C), RS1000099076 (2:158208978 T>C), RS1000100085 (2:158202401 C>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary amenorrhea (MONDO:1060208)

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004069_10	Cerebrospinal fluid AB1-42 levels	9.000000e-06
GCST005042_5	Restless legs syndrome	3.000000e-25
GCST011995_23	Restless legs syndrome	6.000000e-20
GCST012305_20	Major depressive disorder x sex interaction	9.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004670	beta-amyloid 1-42 measurement
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs79048288	CCDC148		0.00	0

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
Aflatoxin B1	decreases methylation, increases methylation	2
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, affects methylation, decreases methylation	1
trichostatin A	affects expression	1
butyraldehyde	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	increases expression	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Fulvestrant	affects methylation, affects cotreatment	1
Vorinostat	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	increases expression	1
Methyl Methanesulfonate	increases expression	1
Tobacco Smoke Pollution	affects expression	1
Gold Compounds	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT07164248	Not specified	COMPLETED	Evaluation of Bone Mineral Density Indications and Outcomes in Female Adolescents: Implications for Early Detection of Osteopenia/Osteoporosis and Gynecologic Practice