CCDC188

Summary

CCDC188 (coiled-coil domain containing 188, HGNC:51899) is a protein-coding gene on chromosome 22q11.21, encoding Coiled-coil domain-containing protein 188 (H7C350).

Predicted to be located in membrane.

Source: NCBI Gene 388849 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001365892

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51899
Approved symbol	CCDC188
Name	coiled-coil domain containing 188
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000234409
Ensembl biotype	protein_coding
Entrez	388849

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000439765, ENST00000444532

RefSeq mRNA: 1 — MANE Select: NM_001365892 NM_001365892

CCDS: CCDS93123

Canonical transcript exons

ENST00000439765 — 9 exons

Exon	Start	End
ENSE00001597219	20150468	20151055
ENSE00001687839	20149724	20149780
ENSE00001724398	20150143	20150250
ENSE00001726623	20148416	20148800
ENSE00001803655	20149955	20150059
ENSE00003490769	20149581	20149640
ENSE00003539712	20148875	20148924
ENSE00003577979	20149412	20149476
ENSE00003675356	20149187	20149244

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 93.00.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0080 / max 7.2174, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193184	0.0080	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	93.00	gold quality
right testis	UBERON:0004534	92.92	gold quality
testis	UBERON:0000473	92.14	gold quality
pituitary gland	UBERON:0000007	88.56	gold quality
sural nerve	UBERON:0015488	86.79	gold quality
adenohypophysis	UBERON:0002196	86.49	gold quality
tibial nerve	UBERON:0001323	80.87	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.50	gold quality
mucosa of stomach	UBERON:0001199	77.97	gold quality
cerebellar hemisphere	UBERON:0002245	77.73	gold quality
cerebellar cortex	UBERON:0002129	77.53	gold quality
cerebellum	UBERON:0002037	77.47	gold quality
hypothalamus	UBERON:0001898	77.09	gold quality
stromal cell of endometrium	CL:0002255	76.15	gold quality
right frontal lobe	UBERON:0002810	74.16	gold quality
primary visual cortex	UBERON:0002436	73.48	gold quality
apex of heart	UBERON:0002098	73.35	gold quality
superior frontal gyrus	UBERON:0002661	72.72	gold quality
subcutaneous adipose tissue	UBERON:0002190	72.06	gold quality
left ovary	UBERON:0002119	71.97	gold quality
brain	UBERON:0000955	71.62	gold quality
frontal cortex	UBERON:0001870	71.25	gold quality
nucleus accumbens	UBERON:0001882	70.92	gold quality
right ovary	UBERON:0002118	70.87	gold quality
spleen	UBERON:0002106	70.30	gold quality
ovary	UBERON:0000992	70.06	gold quality
left uterine tube	UBERON:0001303	70.03	gold quality
Brodmann (1909) area 9	UBERON:0013540	69.85	gold quality
adipose tissue	UBERON:0001013	69.53	gold quality
prefrontal cortex	UBERON:0000451	69.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.37

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc188	ENSMUSG00000090777
rattus_norvegicus	Ccdc188	ENSRNOG00000042711

Paralogs (2): SMCO2 (ENSG00000165935), TMCO5A (ENSG00000166069)

Protein

Protein identifiers

Coiled-coil domain-containing protein 188 — H7C350 (reviewed: H7C350)

All UniProt accessions (1): H7C350

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001352821* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026617	SMCO2/5	Family

UniProt features (6 total): region of interest 3, chain 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H7C350-F1	61.90	0.22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 31 (showing top): GOBP_SINGLE_FERTILIZATION, GOBP_MALE_GAMETE_GENERATION, GOBP_NUCLEUS_ORGANIZATION, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_SPERMATID_NUCLEUS_DIFFERENTIATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_FERTILIZATION, GOBP_MITOCHONDRION_ORGANIZATION, GOBP_MICROTUBULE_BASED_MOVEMENT

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

48 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC188	EXTL2	Q9UBQ6	578
CCDC188	PPP1R21	Q6ZMI0	571
CCDC188	DACT2	Q5SW24	521
CCDC188	ENSA	O43768	514
CCDC188	TOP6BL	Q8N6T0	507
CCDC188	ZNF165	P49910	471
CCDC188	DDR1	Q08345	368
CCDC188	PBX2	P40425	352
CCDC188	CADM2	Q8N3J6	336
CCDC188	EXOC4	Q96A65	321
CCDC188	CALU	O43852	314
CCDC188	DPY19L1	Q2PZI1	276
CCDC188	STOML1	Q9UBI4	256
CCDC188	SLC7A14	Q8TBB6	220
CCDC188	MYOM3	Q5VTT5	215

IntAct

0 interactions, top by confidence:

BioGRID (1): ATP5A1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GVZ6, A0A1W2PPE3, A0A1W2PR82, A2VE02, A5D7I0, A6NDZ8, A6NE82, A6NJ08, A6NJB7, A6NJI1, A6QP24, A6QPM6, A8MUA0, A8MV72, A8MYA2, B2RW88, B7ZNG4, H7C350, O94850, P24097, P50617, Q0P5M0, Q0VD86, Q2KIL8, Q3SY00, Q3SYA9, Q3UN58, Q3ZBU3, Q3ZCQ2, Q5BMD4, Q5JTZ5, Q5M844, Q5RBE4, Q5VZ46, Q66MI6, Q6PAC4, Q80TS7, Q80VY2, Q8BFY7, Q8BT88

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

901 predictions. Top by Δscore:

Variant	Effect	Δscore
22:20149409:TA:T	donor_loss	1.0000
22:20149410:A:C	donor_loss	1.0000
22:20149411:C:CG	donor_loss	1.0000
22:20149638:CAC:C	acceptor_gain	1.0000
22:20149639:ACC:A	acceptor_loss	1.0000
22:20149642:T:A	acceptor_loss	1.0000
22:20149410:A:AC	donor_gain	0.9900
22:20149411:C:CC	donor_gain	0.9900
22:20149636:CACAC:C	acceptor_gain	0.9900
22:20149981:G:A	donor_gain	0.9900
22:20150060:C:CC	acceptor_gain	0.9900
22:20148765:A:T	acceptor_gain	0.9800
22:20148798:AGCC:A	acceptor_loss	0.9800
22:20148799:GCCT:G	acceptor_loss	0.9800
22:20148801:C:CC	acceptor_gain	0.9800
22:20149477:C:CC	acceptor_gain	0.9800
22:20149641:C:CC	acceptor_gain	0.9800
22:20148797:CAGC:C	acceptor_gain	0.9700
22:20148800:CCT:C	acceptor_loss	0.9700
22:20148801:C:CG	acceptor_loss	0.9700
22:20148802:T:C	acceptor_loss	0.9700
22:20149475:TT:T	acceptor_gain	0.9700
22:20149486:A:T	acceptor_gain	0.9700
22:20149575:ACCT:A	donor_loss	0.9700
22:20149577:CTAC:C	donor_loss	0.9700
22:20149578:TAC:T	donor_loss	0.9700
22:20149579:ACCAG:A	donor_loss	0.9700
22:20149580:CCAGG:C	donor_loss	0.9700
22:20149637:ACAC:A	acceptor_gain	0.9700
22:20149638:CACC:C	acceptor_gain	0.9700

AlphaMissense

2554 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:20149751:A:C	F254L	0.983
22:20149751:A:T	F254L	0.983
22:20149753:A:G	F254L	0.983
22:20149731:A:G	I261T	0.972
22:20149731:A:C	I261S	0.971
22:20149764:A:G	I250T	0.971
22:20150188:G:C	F194L	0.970
22:20150188:G:T	F194L	0.970
22:20150190:A:G	F194L	0.970
22:20149773:A:G	L247P	0.969
22:20149742:C:A	K257N	0.967
22:20149742:C:G	K257N	0.967
22:20150231:A:G	L180P	0.963
22:20149731:A:T	I261N	0.960
22:20149752:A:G	F254S	0.958
22:20149472:A:G	L285P	0.957
22:20149761:C:G	R251P	0.953
22:20149764:A:C	I250S	0.952
22:20150248:T:A	K174N	0.952
22:20150248:T:G	K174N	0.952
22:20148617:G:C	F402L	0.948
22:20148617:G:T	F402L	0.948
22:20148619:A:G	F402L	0.948
22:20149752:A:C	F254C	0.944
22:20149739:C:A	K258N	0.943
22:20149739:C:G	K258N	0.943
22:20150469:A:G	L173P	0.941
22:20149468:C:A	K286N	0.940
22:20149468:C:G	K286N	0.940
22:20149585:A:G	L282P	0.936

dbSNP variants (sampled 300 via entrez): RS1000621538 (22:20150048 C>G,T), RS1001229463 (22:20151356 C>G,T), RS1003273565 (22:20148522 T>C,G), RS1003330504 (22:20148724 G>A,T), RS1005761962 (22:20150709 C>T), RS1006355629 (22:20152036 C>G,T), RS1006714962 (22:20151797 T>C,G), RS1007308691 (22:20152879 C>T), RS1008466592 (22:20149240 G>A,C), RS1009473791 (22:20150300 G>A), RS1010827942 (22:20152811 T>G), RS1011444473 (22:20152642 G>A,C), RS1012921617 (22:20150358 A>C,G,T), RS1013941211 (22:20150736 T>C), RS1013995778 (22:20151016 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

1 associations (top):

Study	Trait	p-value
GCST006097_13	Moderate to vigorous physical activity levels	2.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008002	physical activity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
Niclosamide	increases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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