CCDC179

Summary

CCDC179 (coiled-coil domain containing 179, HGNC:44653) is a protein-coding gene on chromosome 11p14.3, encoding Coiled-coil domain-containing protein 179 (H3BU77).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 16 total — 1 pathogenic
• MANE Select transcript: NM_001195637

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44653
Approved symbol	CCDC179
Name	coiled-coil domain containing 179
Location	11p14.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000255359
Ensembl biotype	protein_coding
Entrez	100500938

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 retained_intron, 1 protein_coding

ENST00000529466, ENST00000532798

RefSeq mRNA: 1 — MANE Select: NM_001195637 NM_001195637

CCDS: CCDS58127

Canonical transcript exons

ENST00000532798 — 4 exons

Exon	Start	End
ENSE00002145637	22859452	22859496
ENSE00002170227	22857922	22858026
ENSE00002181365	22860377	22860474
ENSE00002196933	22846922	22847521

Expression profiles

Bgee: expression breadth broad, 47 present calls, max score 90.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0618 / max 72.6247, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119018	0.0618	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.98	gold quality
left testis	UBERON:0004533	90.08	gold quality
testis	UBERON:0000473	89.35	gold quality
right testis	UBERON:0004534	89.24	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.39	gold quality
quadriceps femoris	UBERON:0001377	83.72	gold quality
cerebellar vermis	UBERON:0004720	81.46	gold quality
thymus	UBERON:0002370	78.61	silver quality
calcaneal tendon	UBERON:0003701	49.06	gold quality
granulocyte	CL:0000094	45.84	silver quality
corpus callosum	UBERON:0002336	42.76	gold quality
adrenal tissue	UBERON:0018303	42.41	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
skeletal muscle tissue	UBERON:0001134	36.77	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
bone marrow	UBERON:0002371	35.64	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
gall bladder	UBERON:0002110	34.46	gold quality
right lung	UBERON:0002167	34.35	gold quality
liver	UBERON:0002107	33.82	silver quality
muscle tissue	UBERON:0002385	33.58	gold quality
metanephros cortex	UBERON:0010533	32.66	gold quality
urinary bladder	UBERON:0001255	32.29	gold quality
right uterine tube	UBERON:0001302	32.18	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
tonsil	UBERON:0002372	31.39	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
lymph node	UBERON:0000029	30.63	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting CCDC179, 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-126-5P	100.00	72.71	3180
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc179	ENSMUSG00000094445
rattus_norvegicus	Ccdc179	ENSRNOG00000049297

Protein

Protein identifiers

Coiled-coil domain-containing protein 179 — H3BU77 (reviewed: H3BU77)

All UniProt accessions (1): H3BU77

RefSeq proteins (1): NP_001182566* (*=MANE)

Domains & families (InterPro)

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H3BU77-F1	80.41	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): chr11p14, MIR548N, MIR559, MIR548AW, MIR548Y, MIR548BB_5P, MIR548AR_5P, MIR548AD_5P_MIR548AE_5P_MIR548AY_5P_MIR548B_5P_MIR548D_5P, MIR548AK_MIR548AM_5P_MIR548C_5P_MIR548H_5P_MIR548O_5P_MIR548AU_5P, MIR548O_5P_MIR548W, MIR548AB, MIR548AS_5P, MIR548A_5P, MIR548AQ_5P, MIR548I

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

18 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC179	PTER	Q96BW5	530
CCDC179	NIBAN1	Q9BZQ8	477
CCDC179	DNAH5	Q8TE73	444
CCDC179	AATF	Q9NY61	232
CCDC179	CAPZB	P47756	202
CCDC179	IGF1R	P08069	172
CCDC179	IDH3G	P51553	156
CCDC179	SAMD4B	Q5PRF9	0
CCDC179	PPARA	Q07869	0

IntAct

10 interactions, top by confidence:

A	B	Type	Score
CCDC179	SAMD4B	psi-mi:“MI:0915”(physical association)	0.560
	CCDC179	psi-mi:“MI:0915”(physical association)	0.560
CCDC179	ZNF655	psi-mi:“MI:0915”(physical association)	0.560
CCDC179		psi-mi:“MI:0915”(physical association)	0.000
CCDC179	ZNF655	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): CCDC179 (Two-hybrid), CCDC179 (Two-hybrid), CCDC179 (Two-hybrid)

ESM2 similar proteins: A0A1B0GU33, A0A1B0GUV7, A6NGY3, A6ZT44, F5HHT4, G2TRR6, H3BU77, O13894, O54835, O89085, P0C2W9, P0C6G1, P0C6G2, P0C6G3, P0C6G4, P0C6G5, P0C733, P0DON5, P0DON6, P14976, P16722, P27262, P27271, P28979, P29887, P38612, P38839, Q05105, Q08588, Q1KN14, Q1KN19, Q1X6Y3, Q1X6Y4, Q1X6Z0, Q2YDL7, Q5R5R7, Q5ZK14, Q67621, Q6W0C5, Q88891

Diamond homologs: H3BU77, J3QM76

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	13
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
685359	GRCh37/hg19 11p14.3(chr11:22619798-23441691)x1	Pathogenic

SpliceAI

526 predictions. Top by Δscore:

Variant	Effect	Δscore
11:22847522:C:CC	acceptor_gain	1.0000
11:22857920:A:AC	donor_gain	1.0000
11:22857921:C:CC	donor_gain	1.0000
11:22857921:CT:C	donor_gain	1.0000
11:22858029:T:TC	acceptor_gain	1.0000
11:22858038:T:TC	acceptor_gain	1.0000
11:22847519:CCA:C	acceptor_gain	0.9900
11:22847520:CA:C	acceptor_gain	0.9900
11:22847520:CAC:C	acceptor_gain	0.9900
11:22847532:T:TC	acceptor_gain	0.9900
11:22857913:TATAC:T	donor_loss	0.9900
11:22857914:ATACT:A	donor_loss	0.9900
11:22857915:TACTT:T	donor_loss	0.9900
11:22857916:AC:A	donor_loss	0.9900
11:22857917:C:G	donor_loss	0.9900
11:22857918:T:TA	donor_loss	0.9900
11:22857919:TACT:T	donor_loss	0.9900
11:22857920:ACT:A	donor_loss	0.9900
11:22857921:CTA:C	donor_gain	0.9900
11:22857921:CTAG:C	donor_gain	0.9900
11:22857921:CTAGG:C	donor_gain	0.9900
11:22857955:TGAAA:T	donor_gain	0.9900
11:22858023:CAAG:C	acceptor_gain	0.9900
11:22858025:AGCT:A	acceptor_loss	0.9900
11:22858027:C:CC	acceptor_gain	0.9900
11:22858028:T:C	acceptor_gain	0.9900
11:22858029:T:C	acceptor_gain	0.9900
11:22858038:T:C	acceptor_gain	0.9900
11:22860375:A:AC	donor_gain	0.9900
11:22860376:C:CC	donor_gain	0.9900

AlphaMissense

436 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:22857958:A:C	F53L	0.953
11:22857958:A:T	F53L	0.953
11:22857960:A:G	F53L	0.953
11:22857979:C:A	K46N	0.884
11:22857979:C:G	K46N	0.884
11:22858013:C:G	R35P	0.883
11:22857992:A:G	L42P	0.875
11:22857959:A:G	F53S	0.870
11:22858010:A:G	I36T	0.855
11:22857971:A:G	L49P	0.840
11:22857964:T:A	K51N	0.831
11:22857964:T:G	K51N	0.831
11:22857959:A:C	F53C	0.823
11:22858010:A:C	I36S	0.810
11:22857965:T:A	K51I	0.768
11:22858001:A:G	M39T	0.753
11:22860416:G:C	C2W	0.738
11:22857985:T:A	K44N	0.732
11:22857985:T:G	K44N	0.732
11:22860418:A:G	C2R	0.726
11:22857986:T:A	K44I	0.722
11:22857930:C:G	G63R	0.720
11:22857930:C:T	G63R	0.720
11:22857980:T:G	K46T	0.710
11:22858014:G:T	R35S	0.694
11:22857988:C:A	K43N	0.689
11:22857988:C:G	K43N	0.689
11:22858010:A:T	I36N	0.687
11:22857960:A:C	F53V	0.685
11:22857926:A:G	L64P	0.680

dbSNP variants (sampled 300 via entrez): RS1000005473 (11:22849978 C>T), RS1000413575 (11:22858461 C>G), RS1000427996 (11:22856120 A>G), RS1000695709 (11:22861054 T>C), RS1000947447 (11:22850168 C>A), RS1001163142 (11:22854663 A>G), RS1001618835 (11:22853526 A>G), RS1001677050 (11:22848893 T>C), RS1001689681 (11:22859778 G>A), RS1002005851 (11:22847767 A>T), RS1002109472 (11:22859980 T>C), RS1002256707 (11:22853472 G>A,T), RS1002363497 (11:22859823 T>C,G), RS1002565848 (11:22847815 A>G), RS1002793831 (11:22858959 A>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:600057

GenCC curated gene-disease

Mondo (1): bladder exstrophy-epispadias-cloacal exstrophy complex (MONDO:0700039)

Orphanet (1): Classic bladder exstrophy (Orphanet:93930)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009997_8	Thyroid volume in Hashimoto’s thyroiditis	7.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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