CCDC149

Summary

CCDC149 (coiled-coil domain containing 149, HGNC:25405) is a protein-coding gene on chromosome 4p15.2, encoding Coiled-coil domain-containing protein 149 (Q6ZUS6).

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 95 total
• MANE Select transcript: NM_001395273

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25405
Approved symbol	CCDC149
Name	coiled-coil domain containing 149
Location	4p15.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761B107
Ensembl gene	ENSG00000181982
Ensembl biotype	protein_coding
Entrez	91050

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000324309, ENST00000389609, ENST00000502801, ENST00000504487, ENST00000507096, ENST00000508236, ENST00000512432, ENST00000635206, ENST00000904724, ENST00000904725, ENST00000904726, ENST00000904727, ENST00000914099, ENST00000951414

RefSeq mRNA: 4 — MANE Select: NM_001395273 NM_001130726, NM_001330644, NM_001395273, NM_173463

CCDS: CCDS33967, CCDS47036, CCDS82914

Canonical transcript exons

ENST00000635206 — 13 exons

Exon	Start	End
ENSE00002058659	24803514	24808819
ENSE00003303606	24822497	24822573
ENSE00003305672	24831506	24831650
ENSE00003455803	24819859	24819975
ENSE00003462866	24834948	24835032
ENSE00003485178	24876536	24876697
ENSE00003499056	24837228	24837400
ENSE00003538896	24873681	24873719
ENSE00003550646	24853072	24853179
ENSE00003599779	24838156	24838272
ENSE00003653131	24836436	24836508
ENSE00003785313	24821055	24821087
ENSE00003785619	24912817	24913042

Expression profiles

Bgee: expression breadth ubiquitous, 227 present calls, max score 95.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2938 / max 115.0268, expressed in 1545 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
51677	7.0359	1541
51676	0.2579	130

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	95.62	gold quality
sural nerve	UBERON:0015488	91.41	gold quality
calcaneal tendon	UBERON:0003701	88.88	gold quality
pancreatic ductal cell	CL:0002079	88.82	silver quality
body of pancreas	UBERON:0001150	88.49	gold quality
monocyte	CL:0000576	87.30	gold quality
mucosa of stomach	UBERON:0001199	87.06	gold quality
right uterine tube	UBERON:0001302	86.82	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.68	gold quality
leukocyte	CL:0000738	86.67	gold quality
lower esophagus	UBERON:0013473	86.62	gold quality
pancreas	UBERON:0001264	86.49	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.85	gold quality
tendon	UBERON:0000043	85.72	gold quality
tibial nerve	UBERON:0001323	85.36	gold quality
body of stomach	UBERON:0001161	85.13	gold quality
anterior cingulate cortex	UBERON:0009835	84.98	gold quality
right frontal lobe	UBERON:0002810	84.89	gold quality
body of uterus	UBERON:0009853	84.73	gold quality
ascending aorta	UBERON:0001496	84.35	gold quality
popliteal artery	UBERON:0002250	84.29	gold quality
tibial artery	UBERON:0007610	84.29	gold quality
thoracic aorta	UBERON:0001515	84.27	gold quality
islet of Langerhans	UBERON:0000006	84.19	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.19	gold quality
aorta	UBERON:0000947	84.17	gold quality
stomach	UBERON:0000945	84.13	gold quality
saliva-secreting gland	UBERON:0001044	84.06	gold quality
cerebellar hemisphere	UBERON:0002245	84.06	gold quality
prefrontal cortex	UBERON:0000451	84.02	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.16
E-ENAD-17	no	155.41
E-GEOD-100618	no	52.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

104 targeting CCDC149, 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-4795-3P	100.00	74.62	4024
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-149-3P	99.72	68.22	3963

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc149b	ENSDARG00000020857
danio_rerio	ccdc149a	ENSDARG00000078829
mus_musculus	Ccdc149	ENSMUSG00000045790
rattus_norvegicus	Ccdc149	ENSRNOG00000024454
drosophila_melanogaster	CG14868	FBGN0038330
caenorhabditis_elegans		WBGENE00009258

Protein

Protein identifiers

Coiled-coil domain-containing protein 149 — Q6ZUS6 (reviewed: Q6ZUS6)

All UniProt accessions (4): Q6ZUS6, A0A0U1RQD2, A0A8V8PSJ6, A0A8V8PVV8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CCDC149 family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q6ZUS6-1	1	yes
Q6ZUS6-2	2
Q6ZUS6-3	3
Q6ZUS6-4	4
Q6ZUS6-5	5
Q6ZUS6-6	6

RefSeq proteins (4): NP_001124198, NP_001317573, NP_001382202, NP_775734 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019179	CC149	Family

Pfam: PF09789

UniProt features (15 total): splice variant 6, coiled-coil region 3, region of interest 2, compositionally biased region 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZUS6-F1	69.52	0.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): NKX25_02, RYTTCCTG_ETS2_B, TAATTA_CHX10_01, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, chr4p15, ZWANG_EGF_PERSISTENTLY_UP, LHX9_TARGET_GENES, ZNF711_TARGET_GENES, MIR4795_3P, MIR126_5P, MIR6876_5P, MIR4476, MIR330_5P, MIR7114_5P, MIR3192_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

312 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC149	RMDN2	Q96LZ7	599
CCDC149	DLGAP1	P78335	540
CCDC149	SRGAP2	O75044	538
CCDC149	DRC11	Q86XH1	531
CCDC149	ADGB	Q8N7X0	521
CCDC149	MYO10	Q9HD67	516
CCDC149	PPP2R5C	Q13362	515
CCDC149	SRGAP3	O43295	511
CCDC149	LGI2	Q8N0V4	484
CCDC149	ANAPC4	Q9UJX5	475
CCDC149	PPP1R21	Q6ZMI0	474
CCDC149	SLC36A1	Q7Z2H8	462
CCDC149	GTF2IRD1	Q9UHL9	462
CCDC149	ULK4	Q96C45	461
CCDC149	CTBP1	Q13363	459

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CCDC149	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
CCDC149	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
MKNK1	SEC16A	psi-mi:“MI:0914”(association)	0.350
PRNP	CCDC149	psi-mi:“MI:0407”(direct interaction)	0.000

BioGRID (6): CCDC149 (Reconstituted Complex), CCDC149 (Reconstituted Complex), CCDC149 (Affinity Capture-MS), CCDC149 (Affinity Capture-RNA), CCDC149 (Reconstituted Complex), APP (Reconstituted Complex)

ESM2 similar proteins: A0A088MLT8, A2AQ25, B3KU38, B5DF41, E9PSK7, O15079, O35274, P0DPB3, P0DPB4, P12755, P49140, P85299, Q0D2I5, Q14DQ1, Q1LY51, Q3B7M3, Q3SYW5, Q4KMA0, Q4R3X1, Q50H33, Q5F3L9, Q5FVG6, Q5RD40, Q5XKK7, Q60698, Q6ZNC4, Q6ZUS6, Q6ZWB6, Q80U23, Q80U62, Q80XA6, Q812A5, Q86YI8, Q8BXL9, Q8K2W6, Q8ND83, Q8NFH8, Q8QFX1, Q8TEK3, Q924W7

Diamond homologs: Q0VCP9, Q5XJA2, Q6DH86, Q6NRH3, Q6ZUS6, Q93635

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	73
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3216 predictions. Top by Δscore:

Variant	Effect	Δscore
4:24808815:CTCCC:C	acceptor_gain	1.0000
4:24808816:TCCC:T	acceptor_gain	1.0000
4:24808817:CCC:C	acceptor_gain	1.0000
4:24808817:CCCC:C	acceptor_gain	1.0000
4:24808818:CC:C	acceptor_gain	1.0000
4:24808818:CCC:C	acceptor_gain	1.0000
4:24808819:CC:C	acceptor_gain	1.0000
4:24808819:CCT:C	acceptor_loss	1.0000
4:24808820:C:CC	acceptor_gain	1.0000
4:24808820:C:T	acceptor_gain	1.0000
4:24819853:GCTTA:G	donor_loss	1.0000
4:24819854:CTTA:C	donor_loss	1.0000
4:24819855:TTACC:T	donor_loss	1.0000
4:24819856:TA:T	donor_loss	1.0000
4:24819857:A:AC	donor_gain	1.0000
4:24819857:ACCAT:A	donor_gain	1.0000
4:24819858:C:CC	donor_gain	1.0000
4:24819858:CCAT:C	donor_gain	1.0000
4:24819858:CCATC:C	donor_gain	1.0000
4:24819971:GCCCC:G	acceptor_gain	1.0000
4:24819972:CCCC:C	acceptor_gain	1.0000
4:24819972:CCCCC:C	acceptor_gain	1.0000
4:24819973:CCC:C	acceptor_gain	1.0000
4:24819973:CCCC:C	acceptor_gain	1.0000
4:24819974:CC:C	acceptor_gain	1.0000
4:24819974:CCC:C	acceptor_gain	1.0000
4:24819975:CC:C	acceptor_gain	1.0000
4:24819976:C:CC	acceptor_gain	1.0000
4:24819977:T:A	acceptor_loss	1.0000
4:24819979:T:C	acceptor_gain	1.0000

AlphaMissense

3542 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000005494 (4:24807999 T>A,C), RS10000087 (4:24805568 G>A), RS10000139 (4:24870759 C>T), RS1000016712 (4:24872511 A>G), RS1000069942 (4:24886644 C>T), RS1000078016 (4:24906640 C>T), RS1000141588 (4:24897746 G>T), RS1000157585 (4:24820672 C>A), RS1000171665 (4:24979632 C>G), RS1000177144 (4:24949938 C>G), RS1000212340 (4:24899091 G>A,C), RS1000214816 (4:24904285 T>C), RS1000230737 (4:24838483 G>T), RS1000238355 (4:24878733 C>T), RS10002411 (4:24876868 C>A,G,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

9 associations (top):

Study	Trait	p-value
GCST002579_4	Heschl’s gyrus morphology	4.000000e-06
GCST004766_6	Triglyceride change in response to fenofibrate in statin-treated type 2 diabetes	3.000000e-07
GCST005588_23	Idiopathic dilated cardiomyopathy	7.000000e-06
GCST007202_11	High density lipoprotein cholesterol levels	4.000000e-06
GCST007658_4	Triglyceride levels (parental genotype effect)	3.000000e-07
GCST007658_5	Triglyceride levels (parental genotype effect)	1.000000e-07
GCST007658_6	Triglyceride levels (parental genotype effect)	7.000000e-07
GCST008153_62	Lean body mass	5.000000e-07
GCST009305_15	California verbal learning test score	1.000000e-06

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0007681	triglyceride change measurement
EFO:0009094	idiopathic dilated cardiomyopathy
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004530	triglyceride measurement
EFO:0005939	parental genotype effect measurement
EFO:0004995	lean body mass
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression	2
Nickel	decreases expression	2
Valproic Acid	affects expression, decreases expression	2
Particulate Matter	increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
trichostatin A	affects expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	decreases expression, affects cotreatment	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Fulvestrant	decreases methylation	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Estradiol	affects expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Thiram	increases expression	1
Cyclosporine	increases expression	1
Asbestos, Serpentine	decreases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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