CCDC172

Summary

CCDC172 (coiled-coil domain containing 172, HGNC:30524) is a protein-coding gene on chromosome 10q25.3, encoding Coiled-coil domain-containing protein 172 (P0C7W6).

Predicted to be located in sperm midpiece. Predicted to be active in cytoplasm.

Source: NCBI Gene 374355 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_198515

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30524
Approved symbol	CCDC172
Name	coiled-coil domain containing 172
Location	10q25.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC35062
Ensembl gene	ENSG00000182645
Ensembl biotype	protein_coding
Entrez	374355

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000333254, ENST00000463594, ENST00000497093, ENST00000938958, ENST00000938959

RefSeq mRNA: 1 — MANE Select: NM_198515 NM_198515

CCDS: CCDS31291

Canonical transcript exons

ENST00000333254 — 9 exons

Exon	Start	End
ENSE00001299071	116342036	116342201
ENSE00001309828	116324947	116325090
ENSE00001319920	116340734	116340850
ENSE00001331491	116378423	116378510
ENSE00001331495	116357836	116357938
ENSE00001331501	116357380	116357481
ENSE00001331512	116379323	116380029
ENSE00001331516	116324448	116324613
ENSE00003663675	116325303	116325388

Expression profiles

Bgee: expression breadth broad, 40 present calls, max score 86.57.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0477 / max 22.1032, expressed in 13 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
107189	0.0325	9
107188	0.0151	5

Top tissues by expression

210 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	86.57	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.56	gold quality
right testis	UBERON:0004534	82.28	gold quality
left testis	UBERON:0004533	81.59	gold quality
testis	UBERON:0000473	79.88	gold quality
sperm	CL:0000019	61.56	gold quality
epithelium of nasopharynx	UBERON:0001951	57.93	gold quality
trigeminal ganglion	UBERON:0001675	55.88	silver quality
nasal cavity epithelium	UBERON:0005384	53.46	gold quality
adult organism	UBERON:0007023	52.90	gold quality
quadriceps femoris	UBERON:0001377	51.08	gold quality
upper leg skin	UBERON:0004262	51.05	silver quality
vastus lateralis	UBERON:0001379	50.93	gold quality
oocyte	CL:0000023	50.11	gold quality
skin of hip	UBERON:0001554	48.25	silver quality
body of pancreas	UBERON:0001150	46.84	gold quality
cardia of stomach	UBERON:0001162	45.99	gold quality
pancreas	UBERON:0001264	44.17	gold quality
subthalamic nucleus	UBERON:0001906	43.73	gold quality
inferior vagus X ganglion	UBERON:0005363	43.73	gold quality
dorsal plus ventral thalamus	UBERON:0001897	43.66	gold quality
ventral tegmental area	UBERON:0002691	43.41	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
superior surface of tongue	UBERON:0007371	43.20	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
granulocyte	CL:0000094	42.26	silver quality
superior vestibular nucleus	UBERON:0007227	41.57	gold quality
mammalian vulva	UBERON:0000997	41.34	gold quality
pigmented layer of retina	UBERON:0001782	41.34	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting CCDC172, 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-6798-5P	100.00	65.77	699
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-4777-5P	99.33	67.53	1148
HSA-MIR-320A-5P	98.88	66.75	1248
HSA-MIR-6715B-3P	98.80	68.07	1204
HSA-MIR-4272	98.76	68.74	1810
HSA-MIR-3945	98.68	64.21	553
HSA-MIR-4646-3P	98.65	66.98	693
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-3192-3P	98.62	65.80	970
HSA-MIR-1237-3P	98.55	67.65	1423
HSA-MIR-1248	98.47	67.54	1314
HSA-MIR-6771-3P	98.20	66.53	971
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-1306-5P	97.11	64.04	755
HSA-MIR-125B-2-3P	96.69	68.38	1210
HSA-MIR-4680-5P	96.43	67.15	893
HSA-MIR-4704-5P	96.13	68.67	608
HSA-MIR-4330	95.44	66.39	993
HSA-MIR-12115	94.19	66.37	738

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc172	ENSDARG00000039937
mus_musculus	Ccdc172	ENSMUSG00000025090
rattus_norvegicus	Ccdc172	ENSRNOG00000017656

Protein

Protein identifiers

Coiled-coil domain-containing protein 172 — P0C7W6 (reviewed: P0C7W6)

All UniProt accessions (1): P0C7W6

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. May interact with TEKT2.

Subcellular location. Cytoplasm. Cell projection. Cilium.

Similarity. Belongs to the CCDC172 family.

RefSeq proteins (1): NP_940917* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029618	CCDC172	Family

UniProt features (4 total): coiled-coil region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7W6-F1	88.63	0.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOCC_MOTILE_CILIUM, chr10q25, GOCC_SPERM_MIDPIECE, GOCC_CILIUM, FOSTER_KDM1A_TARGETS_UP, GOCC_9PLUS2_MOTILE_CILIUM, GSE13522_WT_VS_IFNG_KO_SKIN_UP, HMGA1_TARGET_GENES, MIR6868_3P, MIR1248, MIR4777_5P, MIR4330

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): cytoplasm (GO:0005737), sperm midpiece (GO:0097225), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
binding	1
intracellular anatomical structure	1
sperm flagellum	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

176 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC172	C10orf53	Q8N6V4	596
CCDC172	ZNF730	Q6ZMV8	574
CCDC172	CFAP184	Q2M329	571
CCDC172	LRMDA	Q9H2I8	568
CCDC172	CIMIP2B	A8MTA8	520
CCDC172	THNSL2	Q86YJ6	489
CCDC172	SLC14A2	Q15849	473
CCDC172	TTC23	Q5W5X9	447
CCDC172	NUTM2A	Q8IVF1	419
CCDC172	CEP295	Q9C0D2	418
CCDC172	TMEM17	Q86X19	417
CCDC172	LRRC34	Q8IZ02	417
CCDC172	CC2D1A	Q6P1N0	386
CCDC172	MAPKBP1	O60336	376
CCDC172	DEUP1	Q05D60	370
CCDC172	C7	P10643	370

IntAct

76 interactions, top by confidence:

A	B	Type	Score
CCDC172	TCHP	psi-mi:“MI:0915”(physical association)	0.780
TCHP	CCDC172	psi-mi:“MI:0915”(physical association)	0.780
CCDC172	DCTN2	psi-mi:“MI:0915”(physical association)	0.670
CCDC172	HDDC3	psi-mi:“MI:0915”(physical association)	0.670
FAM13C	CCDC172	psi-mi:“MI:0915”(physical association)	0.670
CCDC172	SMARCE1	psi-mi:“MI:0915”(physical association)	0.670
DCTN2	CCDC172	psi-mi:“MI:0915”(physical association)	0.670
CCDC172	FAM13C	psi-mi:“MI:0915”(physical association)	0.670
SMARCE1	CCDC172	psi-mi:“MI:0915”(physical association)	0.670
HDDC3	CCDC172	psi-mi:“MI:0915”(physical association)	0.670
CCDC172	TEAD4	psi-mi:“MI:0915”(physical association)	0.560
TXNDC9	CCDC172	psi-mi:“MI:0915”(physical association)	0.560
CCDC172	ISCU	psi-mi:“MI:0915”(physical association)	0.560
SH2D4A	CCDC172	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (37): CCDC172 (Two-hybrid), CCDC172 (Two-hybrid), CCDC172 (Two-hybrid), CCDC172 (Two-hybrid), CCDC172 (Two-hybrid), CCDC172 (Two-hybrid), CCDC172 (Two-hybrid), CCDC172 (Two-hybrid), HDDC3 (Two-hybrid), PLEKHF2 (Two-hybrid), CCDC122 (Affinity Capture-MS), NINL (Affinity Capture-MS), MIPOL1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), BBS4 (Affinity Capture-MS)

ESM2 similar proteins: A2A2Z9, A6NC57, A8MYB1, A9JSR5, A9ZSY0, D3ZNV2, E9PVB3, O94252, P0A1K3, P0A1K4, P0C221, P0C7W6, Q01649, Q08B20, Q0VBY1, Q10006, Q10221, Q1MTQ0, Q2T9Z6, Q2TA00, Q2YDH9, Q3KPU6, Q5AI71, Q5BJE1, Q5I0J4, Q5PQJ9, Q5T0U0, Q5VUR7, Q66HB6, Q6AXT4, Q6AY08, Q6GM07, Q80X59, Q810N9, Q8BVM7, Q8BVN0, Q8CDV0, Q8IVF6, Q8IWF9, Q8N6Q1

Diamond homologs: P0C7W6, Q2YDH9, Q3KPU6, Q6AXT4, Q810N9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1490 predictions. Top by Δscore:

Variant	Effect	Δscore
10:116325067:A:T	donor_gain	1.0000
10:116340846:CCTTT:C	donor_gain	1.0000
10:116340847:CTTT:C	donor_gain	1.0000
10:116340851:G:GG	donor_gain	1.0000
10:116342026:T:G	acceptor_gain	1.0000
10:116342035:GGA:G	acceptor_gain	1.0000
10:116342192:TTGAA:T	donor_gain	1.0000
10:116342199:GTG:G	donor_gain	1.0000
10:116357378:A:AG	acceptor_gain	1.0000
10:116357379:G:GG	acceptor_gain	1.0000
10:116357477:TAAAG:T	donor_loss	1.0000
10:116357478:AAAGG:A	donor_loss	1.0000
10:116357479:AAGGT:A	donor_loss	1.0000
10:116357480:AGG:A	donor_loss	1.0000
10:116357481:GG:G	donor_loss	1.0000
10:116357482:G:GA	donor_loss	1.0000
10:116357483:T:A	donor_loss	1.0000
10:116357831:TTTA:T	acceptor_loss	1.0000
10:116357834:A:AG	acceptor_gain	1.0000
10:116357835:G:GA	acceptor_gain	1.0000
10:116357835:GT:G	acceptor_gain	1.0000
10:116357835:GTT:G	acceptor_gain	1.0000
10:116357935:TAAG:T	donor_loss	1.0000
10:116357938:GGTA:G	donor_loss	1.0000
10:116357939:G:GG	donor_gain	1.0000
10:116378417:A:G	acceptor_gain	1.0000
10:116378419:ATAG:A	acceptor_loss	1.0000
10:116378420:TA:T	acceptor_loss	1.0000
10:116378421:A:AC	acceptor_loss	1.0000
10:116378421:A:AG	acceptor_gain	1.0000

AlphaMissense

1769 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:116325073:G:C	R21P	0.936
10:116325060:G:C	A17P	0.931
10:116342096:T:C	F115L	0.926
10:116342098:T:A	F115L	0.926
10:116342098:T:G	F115L	0.926
10:116378425:T:C	L219P	0.910
10:116342075:T:C	F108L	0.908
10:116342077:T:A	F108L	0.908
10:116342077:T:G	F108L	0.908
10:116325028:T:C	L6P	0.896
10:116378482:T:C	L238P	0.896
10:116342183:G:C	A144P	0.890
10:116325076:G:C	R22P	0.889
10:116357881:T:C	L199P	0.883
10:116325085:G:C	R25P	0.863
10:116342097:T:C	F115S	0.842
10:116325357:T:C	L45P	0.838
10:116325327:G:C	R35P	0.831
10:116325040:T:G	I10S	0.818
10:116325040:T:C	I10T	0.814
10:116342076:T:C	F108S	0.802
10:116357422:T:C	L164P	0.798
10:116357886:G:C	A201P	0.798
10:116325053:G:C	E14D	0.795
10:116325053:G:T	E14D	0.795
10:116325072:C:A	R21S	0.795
10:116357464:T:C	L178P	0.795
10:116325015:A:C	S2R	0.783
10:116325017:C:A	S2R	0.783
10:116325017:C:G	S2R	0.783

dbSNP variants (sampled 300 via entrez): RS1000001803 (10:116344546 G>T), RS1000067383 (10:116349608 A>C,T), RS1000083662 (10:116356916 A>G), RS1000137259 (10:116330510 T>C), RS1000155564 (10:116324672 G>A), RS1000178967 (10:116356472 G>C), RS1000218420 (10:116372068 T>C), RS1000274677 (10:116358157 A>G), RS1000287177 (10:116363156 C>G), RS1000381567 (10:116364700 A>T), RS1000481556 (10:116369603 A>T), RS1000584926 (10:116329394 T>G), RS1000709043 (10:116324437 C>G,T), RS1000800842 (10:116352863 A>T), RS1000936227 (10:116353049 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:614402, MIM:249000

GenCC curated gene-disease

Mondo (2): microphthalmia, syndromic 11 (MONDO:0013734), Meckel syndrome (MONDO:0018921)

Orphanet (1): Meckel syndrome (Orphanet:564)

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002949_12	Epilepsy and lamotrigine-induced maculopapular eruptions	1.000000e-07
GCST010725_100	Malaria	3.000000e-06
GCST010725_45	Malaria	5.000000e-06
GCST90026412_8	Severe autoimmune type 2 diabetes	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:1001253	maculopapular eruption

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
trichostatin A	increases expression	1
2-palmitoylglycerol	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cadmium	increases abundance, increases expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01401998	Not specified	RECRUITING	ARPKD Database Study