CCDC71

Summary

CCDC71 (coiled-coil domain containing 71, HGNC:25760) is a protein-coding gene on chromosome 3p21.31, encoding Coiled-coil domain-containing protein 71 (Q8IV32).

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_022903

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25760
Approved symbol	CCDC71
Name	coiled-coil domain containing 71
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12800
Ensembl gene	ENSG00000177352
Ensembl biotype	protein_coding
Entrez	64925

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000321895, ENST00000870129, ENST00000870130

RefSeq mRNA: 1 — MANE Select: NM_022903 NM_022903

CCDS: CCDS2790

Canonical transcript exons

ENST00000321895 — 2 exons

Exon	Start	End
ENSE00001263023	49162535	49164260
ENSE00001650748	49166267	49166331

Expression profiles

Bgee: expression breadth ubiquitous, 135 present calls, max score 85.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.7685 / max 128.5350, expressed in 1813 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42225	23.6243	1811
42224	1.1442	854

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	85.46	gold quality
thymus	UBERON:0002370	84.52	silver quality
fallopian tube	UBERON:0003889	84.48	gold quality
mucosa of transverse colon	UBERON:0004991	84.30	gold quality
right adrenal gland	UBERON:0001233	83.97	gold quality
left uterine tube	UBERON:0001303	83.96	gold quality
left adrenal gland	UBERON:0001234	83.65	gold quality
right adrenal gland cortex	UBERON:0035827	83.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.47	gold quality
placenta	UBERON:0001987	83.37	gold quality
left adrenal gland cortex	UBERON:0035825	83.29	gold quality
right lobe of thyroid gland	UBERON:0001119	83.24	gold quality
gastrocnemius	UBERON:0001388	83.00	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.91	gold quality
granulocyte	CL:0000094	82.90	gold quality
blood	UBERON:0000178	82.89	gold quality
muscle of leg	UBERON:0001383	82.87	gold quality
left ovary	UBERON:0002119	82.85	gold quality
ovary	UBERON:0000992	82.78	gold quality
apex of heart	UBERON:0002098	82.78	gold quality
right ovary	UBERON:0002118	82.68	gold quality
muscle tissue	UBERON:0002385	82.48	gold quality
left lobe of thyroid gland	UBERON:0001120	82.44	gold quality
ectocervix	UBERON:0012249	82.39	gold quality
adrenal gland	UBERON:0002369	82.38	gold quality
thyroid gland	UBERON:0002046	82.22	gold quality
endocervix	UBERON:0000458	82.00	gold quality
skeletal muscle tissue	UBERON:0001134	81.91	gold quality
mucosa of stomach	UBERON:0001199	81.89	gold quality
esophagus mucosa	UBERON:0002469	81.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting CCDC71, 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-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-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-4317	98.49	67.09	987
HSA-MIR-6730-5P	98.03	68.12	1299
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-424-3P	97.20	65.86	385
HSA-MIR-411-5P	97.11	66.82	601

Literature-anchored findings (GeneRIF, showing 1)

• ATRX proximal protein associations boast roles beyond histone deposition. (PMID:34780483)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc71	ENSDARG00000071570
mus_musculus	Ccdc71	ENSMUSG00000049305
rattus_norvegicus	Ccdc71	ENSRNOG00000048718

Paralogs (1): CCDC71L (ENSG00000253276)

Protein

Protein identifiers

Coiled-coil domain-containing protein 71 — Q8IV32 (reviewed: Q8IV32)

All UniProt accessions (1): Q8IV32

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (1): NP_075054* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026695	Ccdc71/71L	Family

Pfam: PF15374

UniProt features (12 total): compositionally biased region 4, region of interest 3, sequence variant 2, chain 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IV32-F1	52.59	0.11

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 129

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, GGCNKCCATNK_UNKNOWN, MARTINEZ_RB1_TARGETS_UP, YY1_02, GGAANCGGAANY_UNKNOWN, KMCATNNWGGA_UNKNOWN, HNF4_01, ELK1_01, GGCNNMSMYNTTG_UNKNOWN, GRADE_COLON_AND_RECTAL_CANCER_DN, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, TGGAAA_NFAT_Q4_01, GCCATNTTG_YY1_Q6

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

752 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC71	DYRK2	Q92630	599
CCDC71	ANTXR2	P58335	593
CCDC71	UNC119B	A6NIH7	549
CCDC71	SLX9	Q9NSI2	491
CCDC71	DLK1	P15803	491
CCDC71	ZNF19	P17023	490
CCDC71	EDNRB	P24530	484
CCDC71	DALRD3	Q5D0E6	476
CCDC71	CD79A	P11912	470
CCDC71	ALK	Q9UM73	463
CCDC71	LMBRD2	Q68DH5	456
CCDC71	TMEM69	Q5SWH9	444
CCDC71	LRRC20	Q8TCA0	434
CCDC71	AMZ1	Q400G9	429
CCDC71	WDR6	Q9NNW5	414

IntAct

15 interactions, top by confidence:

A	B	Type	Score
HDAC1	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
RBBP7	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
HDAC1	TNRC18	psi-mi:“MI:0914”(association)	0.790
RBBP7	SMARCA5	psi-mi:“MI:0914”(association)	0.530
H2BC9	CCDC71	psi-mi:“MI:0915”(physical association)	0.400
CCDC71	KRT8	psi-mi:“MI:0915”(physical association)	0.400
CCDC71	SSB	psi-mi:“MI:0915”(physical association)	0.400
CCDC71	TCP1	psi-mi:“MI:0915”(physical association)	0.400
H2BC21	SMCHD1	psi-mi:“MI:0914”(association)	0.350
SSRP1	DDX39A	psi-mi:“MI:0914”(association)	0.350
CCDC71	SUPT5H	psi-mi:“MI:0914”(association)	0.350
CDH5	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (83): CCDC71 (Affinity Capture-MS), CCDC71 (Affinity Capture-MS), CCDC71 (Affinity Capture-MS), CCDC71 (Affinity Capture-MS), CCDC71 (Affinity Capture-MS), CCDC71 (Proximity Label-MS), CCDC71 (Proximity Label-MS), CCDC71 (Proximity Label-MS), CCDC71 (Affinity Capture-RNA), NID2 (Affinity Capture-MS), UNC13B (Affinity Capture-MS), IWS1 (Affinity Capture-MS), HEXIM1 (Affinity Capture-MS), ITPKC (Affinity Capture-MS), GTF2F1 (Affinity Capture-MS)

ESM2 similar proteins: A7RR34, G1SGR6, G1TKB3, H3BMG3, K9NVA6, O18881, O31163, O35817, O46157, O74175, P08798, P0C9Z9, P0CA00, P16458, P25886, P26373, P29548, P41123, P41125, P41128, P41129, P47914, P47915, P47963, P52283, P75588, Q05018, Q09505, Q09507, Q09821, Q13875, Q1K730, Q29187, Q2INT4, Q54CE6, Q54E20, Q54TW3, Q56JZ1, Q58DW3, Q5UPU2

Diamond homologs: Q2HJ91, Q4V7C4, Q8IV32, Q8N9Z2, Q8VEG0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 16 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
NuRD complex assembly	5	50.4×	5e-06
Interaction of NuRD complexes with transcription factors	5	45.3×	5e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

303 predictions. Top by Δscore:

Variant	Effect	Δscore
3:49164264:C:CT	acceptor_gain	1.0000
3:49164265:A:T	acceptor_gain	0.9900
3:49166262:CCTA:C	donor_loss	0.9900
3:49166263:CTA:C	donor_loss	0.9900
3:49166265:A:AC	donor_gain	0.9900
3:49166265:A:T	donor_loss	0.9900
3:49166266:C:A	donor_loss	0.9900
3:49166266:C:CC	donor_gain	0.9900
3:49164264:C:T	acceptor_gain	0.9800
3:49166199:G:A	donor_gain	0.9800
3:49166266:CCGG:C	donor_gain	0.9800
3:49164259:ACC:A	acceptor_loss	0.9600
3:49164261:CT:C	acceptor_loss	0.9600
3:49164262:T:A	acceptor_loss	0.9600
3:49165445:C:A	donor_gain	0.9600
3:49165896:C:A	donor_gain	0.9600
3:49166260:AACCT:A	donor_loss	0.9600
3:49166261:ACCTA:A	donor_loss	0.9600
3:49164269:C:CT	acceptor_gain	0.9500
3:49165807:TCC:T	donor_gain	0.9500
3:49164261:C:CC	acceptor_gain	0.9400
3:49164270:A:T	acceptor_gain	0.9400
3:49164261:C:T	acceptor_gain	0.9200
3:49166017:T:TA	donor_gain	0.9200
3:49166294:G:A	donor_gain	0.9200
3:49165406:AAC:A	donor_gain	0.9100
3:49166022:AGGGC:A	donor_gain	0.9100
3:49165444:C:CA	donor_gain	0.9000
3:49165526:C:A	donor_gain	0.9000
3:49165895:T:TA	donor_gain	0.9000

AlphaMissense

2928 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:49164056:G:C	F51L	0.996
3:49164056:G:T	F51L	0.996
3:49164058:A:G	F51L	0.996
3:49164057:A:G	F51S	0.994
3:49164066:A:G	L48P	0.994
3:49164161:C:A	W16C	0.994
3:49164161:C:G	W16C	0.994
3:49164163:A:G	W16R	0.994
3:49164163:A:T	W16R	0.994
3:49164029:G:C	F60L	0.993
3:49164029:G:T	F60L	0.993
3:49164031:A:G	F60L	0.993
3:49164153:A:G	I19T	0.992
3:49164107:A:C	F34L	0.991
3:49164107:A:T	F34L	0.991
3:49164109:A:G	F34L	0.991
3:49164045:A:G	L55P	0.990
3:49164054:A:G	L52P	0.990
3:49164121:C:G	A30P	0.990
3:49164015:A:G	L65P	0.989
3:49164024:G:T	P62H	0.989
3:49164008:A:C	S67R	0.988
3:49164008:A:T	S67R	0.988
3:49164010:T:G	S67R	0.988
3:49164066:A:T	L48H	0.988
3:49164108:A:G	F34S	0.988
3:49164018:A:T	I64N	0.987
3:49164030:A:G	F60S	0.987
3:49164095:G:C	S38R	0.987
3:49164095:G:T	S38R	0.987

dbSNP variants (sampled 300 via entrez): RS1000452748 (3:49162436 G>A), RS1001717629 (3:49164507 C>T), RS1002388302 (3:49163572 G>A), RS1002399046 (3:49164797 A>G), RS1003061879 (3:49166463 G>A,C), RS1003358904 (3:49166864 A>C,G), RS1003546963 (3:49167702 A>G), RS1003799983 (3:49165194 C>A), RS1003830183 (3:49168189 C>G,T), RS1003840741 (3:49162076 C>A,T), RS1004018953 (3:49168034 G>A), RS1004083161 (3:49162047 C>A), RS1004233667 (3:49165748 C>G,T), RS1006250262 (3:49162909 G>A), RS1006566742 (3:49163310 G>A)

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

12 associations (top):

Study	Trait	p-value
GCST004131_23	Inflammatory bowel disease	1.000000e-33
GCST004132_17	Crohn’s disease	3.000000e-23
GCST004133_11	Ulcerative colitis	8.000000e-20
GCST010698_80	Subcortical volume (min-P)	3.000000e-24
GCST010699_110	Brain morphology (min-P)	4.000000e-08
GCST010701_52	Cortical surface area (MOSTest)	1.000000e-16
GCST010702_36	Subcortical volume (MOSTest)	1.000000e-10
GCST010703_262	Brain morphology (MOSTest)	2.000000e-13
GCST012073_13	Behcet’s disease	3.000000e-07
GCST90020024_1146	A body shape index	4.000000e-08
GCST90020027_106	Waist-hip index	9.000000e-09
GCST90020029_1178	Waist circumference adjusted for body mass index	5.000000e-12

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0007789	BMI-adjusted waist circumference
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, affects binding, increases reaction	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
FR900359	decreases phosphorylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
ferrous chloride	decreases expression	1
coumarin	increases phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
avobenzone	increases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
jinfukang	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, affects expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	increases expression	1
Formaldehyde	decreases expression	1
Ozone	increases abundance, affects expression	1
Potassium Chloride	decreases expression, decreases response to substance	1
Smoke	decreases expression	1
Dronabinol	decreases expression, decreases response to substance	1
Thiram	decreases expression	1
Triiodothyronine	decreases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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