CCDC127

Summary

CCDC127 (coiled-coil domain containing 127, HGNC:30520) is a protein-coding gene on chromosome 5p15.33, encoding Coiled-coil domain-containing protein 127 (Q96BQ5). Regulates lipid droplet homeostasis.

Located in mitochondrion.

Source: NCBI Gene 133957 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 55 total — 1 pathogenic
• MANE Select transcript: NM_145265

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30520
Approved symbol	CCDC127
Name	coiled-coil domain containing 127
Location	5p15.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25701
Ensembl gene	ENSG00000164366
Ensembl biotype	protein_coding
OMIM	621138
Entrez	133957

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000296824, ENST00000441693, ENST00000918339

RefSeq mRNA: 1 — MANE Select: NM_145265 NM_145265

CCDS: CCDS3852

Canonical transcript exons

ENST00000296824 — 3 exons

Exon	Start	End
ENSE00001083877	196868	205958
ENSE00001083879	216729	216859
ENSE00001295592	218093	218153

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 93.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.2042 / max 143.5361, expressed in 1767 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60698	9.2042	1767

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	93.75	gold quality
deltoid	UBERON:0001476	93.10	gold quality
left ventricle myocardium	UBERON:0006566	91.43	silver quality
myocardium	UBERON:0002349	91.08	silver quality
cartilage tissue	UBERON:0002418	90.40	gold quality
biceps brachii	UBERON:0001507	90.25	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	89.81	gold quality
quadriceps femoris	UBERON:0001377	89.43	gold quality
vastus lateralis	UBERON:0001379	89.23	gold quality
pigmented layer of retina	UBERON:0001782	88.92	gold quality
retina	UBERON:0000966	88.90	gold quality
vena cava	UBERON:0004087	88.76	gold quality
seminal vesicle	UBERON:0000998	88.29	gold quality
skeletal muscle tissue	UBERON:0001134	88.26	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	87.53	gold quality
body of tongue	UBERON:0011876	87.36	silver quality
muscle tissue	UBERON:0002385	87.15	gold quality
pericardium	UBERON:0002407	87.14	gold quality
synovial joint	UBERON:0002217	87.11	gold quality
mucosa of paranasal sinus	UBERON:0005030	87.05	silver quality
tongue	UBERON:0001723	87.02	silver quality
superior surface of tongue	UBERON:0007371	86.99	silver quality
subthalamic nucleus	UBERON:0001906	86.90	silver quality
substantia nigra pars compacta	UBERON:0001965	86.80	gold quality
trigeminal ganglion	UBERON:0001675	86.77	gold quality
ventral tegmental area	UBERON:0002691	86.72	gold quality
tendon of biceps brachii	UBERON:0008188	86.67	gold quality
ileal mucosa	UBERON:0000331	86.66	gold quality
lateral globus pallidus	UBERON:0002476	86.66	silver quality
pharyngeal mucosa	UBERON:0000355	86.64	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting CCDC127, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-1324	99.46	66.57	1302
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-767-3P	98.61	67.69	1192
HSA-MIR-4780	98.57	64.75	611
HSA-MIR-4299	98.28	66.96	850
HSA-MIR-3977	98.00	68.17	1500
HSA-MIR-6793-3P	97.66	65.78	1084
HSA-MIR-4689	96.97	65.79	1209
HSA-MIR-6828-3P	96.06	67.61	1155
HSA-MIR-6858-5P	96.05	64.59	1020
HSA-MIR-5002-3P	95.75	67.04	542
HSA-MIR-3162-5P	95.67	67.53	794
HSA-MIR-4462	95.10	66.27	172
HSA-MIR-6514-5P	95.07	66.02	655
HSA-MIR-6816-3P	95.05	66.08	459
HSA-MIR-4633-3P	93.85	63.56	534
HSA-MIR-6500-5P	93.85	63.64	522

Literature-anchored findings (GeneRIF, showing 1)

• A luciferase reporter gene assay revealed that hsp70 promoter activation is enhanced by the transcriptional co-activator AF9 and splicing mediator SNRPE, but suppressed by the coiled-coil domain-containing protein CCDC127. (PMID:26873636)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc127b	ENSDARG00000008946
danio_rerio	ccdc127a	ENSDARG00000104344
mus_musculus	Ccdc127	ENSMUSG00000021578
rattus_norvegicus	Ccdc127	ENSRNOG00000066093

Protein

Protein identifiers

Coiled-coil domain-containing protein 127 — Q96BQ5 (reviewed: Q96BQ5)

All UniProt accessions (2): D6R9R2, Q96BQ5

UniProt curated annotations — full annotation on UniProt →

Function. Regulates lipid droplet homeostasis. May be involved in the adipocyte differentiation.

Subcellular location. Mitochondrion outer membrane.

RefSeq proteins (1): NP_660308* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR034607	CCDC127	Family

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96BQ5-F1	87.32	0.71

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 66 (showing top): TGCGCANK_UNKNOWN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_LIPID_HOMEOSTASIS, WANG_LMO4_TARGETS_DN, GOCC_MITOCHONDRIAL_ENVELOPE, NIKOLSKY_BREAST_CANCER_5P15_AMPLICON, GOBP_HOMEOSTATIC_PROCESS, GOBP_CHEMICAL_HOMEOSTASIS, GOCC_ORGANELLE_ENVELOPE, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, BARX1_TARGET_GENES, ID1_TARGET_GENES, NFE2L1_TARGET_GENES

GO Biological Process (1): lipid homeostasis (GO:0055088)

GO Molecular Function (0):

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chemical homeostasis	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrial membrane	1
organelle outer membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

716 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC127	VCF1	Q969W3	846
CCDC127	TADA2B	Q86TJ2	719
CCDC127	MTO1	Q9Y2Z2	718
CCDC127	SUPT7L	O94864	714
CCDC127	ASB7	Q9H672	714
CCDC127	CNOT10	Q9H9A5	703
CCDC127	SPMIP1	A0A1B0GUX0	640
CCDC127	AARS1	P49588	608
CCDC127	XPNPEP1	Q9NQW7	548
CCDC127	LRRC14B	A6NHZ5	499
CCDC127	CFAP61	Q8NHU2	483
CCDC127	CEBPZOS	A8MTT3	479
CCDC127	CSNK2A2	P19784	473
CCDC127	FBXO48	Q5FWF7	458
CCDC127	ZNF684	Q5T5D7	455

IntAct

35 interactions, top by confidence:

A	B	Type	Score
CHCHD4	SSNA1	psi-mi:“MI:0914”(association)	0.640
PBXIP1	GOLIM4	psi-mi:“MI:0914”(association)	0.530
CCDC127	CETN3	psi-mi:“MI:0914”(association)	0.530
ERBB2	HAX1	psi-mi:“MI:0914”(association)	0.530
CCDC127	ENTREP1	psi-mi:“MI:0915”(physical association)	0.370
CCDC127	RNF11	psi-mi:“MI:0915”(physical association)	0.370
Ckap5	CCHCR1	psi-mi:“MI:0914”(association)	0.350
Rab5c		psi-mi:“MI:0914”(association)	0.350
Rmdn3	DERL1	psi-mi:“MI:0914”(association)	0.350
MYO1C	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Mtx2	NRDC	psi-mi:“MI:0914”(association)	0.350
Tmed2		psi-mi:“MI:0914”(association)	0.350
VAPA		psi-mi:“MI:0914”(association)	0.350
ORF74	MGAT5	psi-mi:“MI:0914”(association)	0.350
CHCHD4	HAX1	psi-mi:“MI:0914”(association)	0.350
CCDC127	GAPDHS	psi-mi:“MI:0914”(association)	0.350
MTCH2	IPO5	psi-mi:“MI:0914”(association)	0.350
SLC16A8	C15orf61	psi-mi:“MI:0914”(association)	0.350
SLC30A7	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC35B2	NDUFS8	psi-mi:“MI:0914”(association)	0.350
ATF2	PLOD2	psi-mi:“MI:0914”(association)	0.350
CEBPA	MYO1C	psi-mi:“MI:0914”(association)	0.350
ERBB2	DNM1L	psi-mi:“MI:0914”(association)	0.350
MYC	AP3B1	psi-mi:“MI:0914”(association)	0.350
STAT3	IDH3B	psi-mi:“MI:0914”(association)	0.350
ATF5	ESYT2	psi-mi:“MI:0914”(association)	0.350
STAT3	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
CEBPA	HAX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (32): CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), CCDC127 (Affinity Capture-MS), VPS16 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), GAPDHS (Affinity Capture-MS)

ESM2 similar proteins: A0A0H3MD02, A4ZU88, A9N5C6, D6YXE8, G2K449, G2TRQ4, H2VFV1, O43087, O84008, O84290, O84621, P07049, P0C267, P0CI27, P0DJO8, P0DPS5, P19200, P27500, P47521, P47522, P59707, P74644, P75395, Q2W8K3, Q3TC33, Q49407, Q57M66, Q5PI48, Q6AX50, Q6P7L0, Q6PEB9, Q722M0, Q7TD11, Q7VI02, Q83AR1, Q83DF6, Q8QL14, Q8Z550, Q8ZNG2, Q92DX9

Diamond homologs: P0C267, Q3TC33, Q6PEB9, Q96BQ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	43
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
148877	GRCh38/hg38 5p15.33(chr5:22149-4260151)x1	Pathogenic

SpliceAI

613 predictions. Top by Δscore:

Variant	Effect	Δscore
5:218123:C:A	donor_gain	1.0000
5:218064:C:CT	donor_gain	0.9900
5:218089:CTA:C	donor_loss	0.9900
5:218092:C:G	donor_loss	0.9900
5:216727:A:AC	donor_gain	0.9800
5:216728:C:CC	donor_gain	0.9800
5:216771:TCC:T	donor_gain	0.9800
5:217982:C:A	donor_gain	0.9800
5:218065:C:CT	donor_gain	0.9800
5:218070:C:A	donor_gain	0.9800
5:218129:A:C	donor_gain	0.9800
5:205964:A:C	acceptor_gain	0.9700
5:218122:T:A	donor_gain	0.9700
5:218128:AACG:A	donor_gain	0.9700
5:205955:CAAC:C	acceptor_gain	0.9600
5:205957:ACC:A	acceptor_loss	0.9600
5:205958:CCTGA:C	acceptor_loss	0.9600
5:205960:T:G	acceptor_loss	0.9600
5:205963:CA:C	acceptor_gain	0.9600
5:205968:A:AC	acceptor_gain	0.9600
5:216772:C:CT	donor_gain	0.9600
5:218069:T:TA	donor_gain	0.9600
5:218094:T:TA	donor_gain	0.9600
5:205964:A:AC	acceptor_gain	0.9500
5:216497:AAT:A	donor_gain	0.9500
5:205299:A:AC	donor_gain	0.9400
5:205300:C:CC	donor_gain	0.9400
5:205954:CCAAC:C	acceptor_gain	0.9400
5:205955:CAACC:C	acceptor_gain	0.9400
5:218132:C:CT	donor_gain	0.9400

AlphaMissense

1704 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:216734:G:T	A39D	0.996
5:216737:G:T	A38D	0.992
5:205445:A:T	I212K	0.991
5:216743:C:T	G36E	0.990
5:216730:A:C	F40L	0.989
5:216730:A:T	F40L	0.989
5:216732:A:G	F40L	0.989
5:216755:A:T	V32D	0.989
5:216744:C:G	G36R	0.987
5:216744:C:T	G36R	0.987
5:216752:G:C	P33R	0.987
5:216752:G:T	P33Q	0.985
5:216774:A:G	W26R	0.985
5:216774:A:T	W26R	0.985
5:216764:G:T	A29D	0.984
5:205573:T:A	R169S	0.983
5:205573:T:G	R169S	0.983
5:216772:C:A	W26C	0.983
5:216772:C:G	W26C	0.983
5:205445:A:C	I212R	0.981
5:216731:A:G	F40S	0.979
5:216740:A:G	L37S	0.979
5:216746:A:T	L35Q	0.979
5:205433:T:A	D216V	0.978
5:205388:C:A	G231V	0.977
5:216758:A:G	L31S	0.977
5:216749:A:T	M34K	0.976
5:205454:A:G	L209P	0.975
5:205956:A:G	W42R	0.975
5:205956:A:T	W42R	0.975

dbSNP variants (sampled 300 via entrez): RS1000113890 (5:205833 G>A), RS1000324545 (5:218527 C>G,T), RS1000556220 (5:197385 C>G), RS1000560376 (5:202184 C>T), RS1000605294 (5:209985 G>C), RS1000692096 (5:198724 G>A), RS1001157580 (5:207089 T>C), RS1001329614 (5:217726 G>A), RS1001450986 (5:217396 GGAT>G), RS1001564047 (5:203153 G>A), RS1001575690 (5:203372 T>C,G), RS1001578397 (5:208506 C>T), RS1001827024 (5:198466 G>A,C), RS1001936704 (5:197689 A>ATTAT), RS1002340506 (5:215820 C>T)

Disease associations

OMIM: gene MIM:621138 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
urushiol	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	increases activity, affects binding, decreases expression	1
bisphenol A	affects cotreatment, increases expression	1
arsenite	affects binding, increases reaction	1
hydroquinone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Potassium Dichromate	decreases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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