CCDC196

Summary

CCDC196 (coiled-coil domain containing 196, HGNC:20100) is a protein-coding gene on chromosome 14q23.3, encoding Coiled-coil domain-containing protein 196 (A0A1B0GTZ2).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001351576

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20100
Approved symbol	CCDC196
Name	coiled-coil domain containing 196
Location	14q23.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000196553
Ensembl biotype	protein_coding
Entrez	440184

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron, 1 protein_coding

ENST00000359454, ENST00000389594, ENST00000411796, ENST00000432289, ENST00000436570, ENST00000450299, ENST00000636229, ENST00000641281, ENST00000641536, ENST00000641713, ENST00000641761, ENST00000641812

RefSeq mRNA: 1 — MANE Select: NM_001351576 NM_001351576

CCDS: CCDS86402

Canonical transcript exons

ENST00000636229 — 10 exons

Exon	Start	End
ENSE00001402198	66486657	66486809
ENSE00001430983	66488987	66489037
ENSE00001506317	66491626	66491685
ENSE00001506318	66490742	66490819
ENSE00001535533	66491021	66491104
ENSE00001604813	66486371	66486552
ENSE00001791965	66488160	66488256
ENSE00003798613	66498109	66498167
ENSE00003799620	66498353	66498553
ENSE00003799738	66492053	66492194

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 99.56.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1079 / max 94.8100, expressed in 7 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
140187	0.0511	6
140188	0.0407	3
140189	0.0160	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.56	gold quality
left testis	UBERON:0004533	96.13	gold quality
right testis	UBERON:0004534	95.59	gold quality
testis	UBERON:0000473	93.04	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.75	gold quality
right lobe of liver	UBERON:0001114	81.84	gold quality
adult organism	UBERON:0007023	79.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.19	gold quality
body of pancreas	UBERON:0001150	71.24	gold quality
liver	UBERON:0002107	69.47	gold quality
calcaneal tendon	UBERON:0003701	69.00	gold quality
mucosa of transverse colon	UBERON:0004991	62.49	gold quality
rectum	UBERON:0001052	62.33	gold quality
pancreas	UBERON:0001264	59.97	gold quality
colonic epithelium	UBERON:0000397	58.53	silver quality
tendon	UBERON:0000043	58.13	gold quality
sural nerve	UBERON:0015488	57.92	silver quality
nucleus accumbens	UBERON:0001882	55.16	gold quality
transverse colon	UBERON:0001157	54.65	gold quality
lower lobe of lung	UBERON:0008949	54.53	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
ileal mucosa	UBERON:0000331	53.97	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
cauda epididymis	UBERON:0004360	53.10	gold quality
epithelial cell of pancreas	CL:0000083	52.85	gold quality
corpus callosum	UBERON:0002336	52.68	gold quality
mucosa of sigmoid colon	UBERON:0004993	52.66	gold quality
bone marrow cell	CL:0002092	52.25	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	32.03
E-ANND-3	yes	4.79

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• LINC00238 inhibits hepatic carcinoma progression by activating TMEM106Cmediated apoptosis pathway. (PMID:34476506)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc196	ENSMUSG00000099418
rattus_norvegicus	Ccdc196	ENSRNOG00000033423

Protein

Protein identifiers

Coiled-coil domain-containing protein 196 — A0A1B0GTZ2 (reviewed: A0A1B0GTZ2)

Alternative names: Long intergenic non-protein coding RNA 238

All UniProt accessions (8): A0A1B0GTZ2, A0A1B0GTP3, A0A1B0GV15, A0A1B0GVV6, A0A1B0GW51, A0A1B0GWI1, A0A286YEX8, A0A286YFE0

RefSeq proteins (1): NP_001338505* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038857	CCDC196	Family

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-A0A1B0GTZ2-F1	68.50	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chr14q23, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN, GSE26495_PD1HIGH_VS_PD1LOW_CD8_TCELL_DN, GSE2128_C57BL6_VS_NOD_CD4CD8_DP_THYMOCYTE_UP

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

54 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC196	GSG1L	Q6UXU4	519
CCDC196	A0A140T9Z0	A0A140T9Z0	507
CCDC196	SLC24A2	Q9UI40	450
CCDC196	C9	P02748	440
CCDC196	C4BPA	P04003	380
CCDC196	ADSS2	P30520	378
CCDC196	ANO2	Q9NQ90	369
CCDC196	PRSS2	P07478	333
CCDC196	FUT8	Q9BYC5	314
CCDC196	KCNE1	P15382	292
CCDC196	CA1	P00915	290
CCDC196	OXT	P01178	286
CCDC196	IL17F	Q96PD4	203
CCDC196	RNF11	Q9Y3C5	185
CCDC196	RPL18	Q07020	171

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTZ2, A3RM20, A4UHQ4, A6H7E2, A6NGH7, A9JSR5, B0BK70, O55527, O74982, P04861, P04862, P06747, P0C137, P0C139, P0C142, P14253, P14254, P33493, P35940, P40167, P69479, P69480, P69738, Q0GBX8, Q13352, Q14BK3, Q2T9U9, Q2YDE5, Q32L17, Q3UYG1, Q4KLZ4, Q4VKV6, Q5I0J4, Q5RE16, Q66HB6, Q6AXY9, Q810N5, Q8IR45, Q8IYM0, Q8NCU1

Diamond homologs: A0A1B0GTZ2, Q2YDE5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1986 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:66488162:T:C	L69P	0.974
14:66486725:T:C	L40P	0.965
14:66486808:A:C	S68R	0.963
14:66488160:T:A	S68R	0.963
14:66488160:T:G	S68R	0.963
14:66489006:T:C	L107P	0.942
14:66488172:G:A	M72I	0.928
14:66488172:G:C	M72I	0.928
14:66488172:G:T	M72I	0.928
14:66486737:T:C	L44P	0.924
14:66488998:C:A	N104K	0.910
14:66488998:C:G	N104K	0.910
14:66486800:A:T	K65I	0.902
14:66486779:T:C	L58S	0.893
14:66488233:G:C	A93P	0.893
14:66486803:A:C	Q66P	0.892
14:66488168:T:G	I71S	0.875
14:66488247:A:C	K97N	0.873
14:66488247:A:T	K97N	0.873
14:66486801:A:C	K65N	0.872
14:66486801:A:T	K65N	0.872
14:66486714:G:C	R36S	0.871
14:66486714:G:T	R36S	0.871
14:66488171:T:C	M72T	0.871
14:66488180:T:C	I75T	0.871
14:66489027:T:C	L114P	0.870
14:66488180:T:G	I75S	0.868
14:66488255:T:C	L100S	0.855
14:66488168:T:C	I71T	0.853
14:66488994:A:T	K103I	0.849

dbSNP variants (sampled 300 via entrez): RS1000119037 (14:66487827 A>T), RS1000156180 (14:66488480 A>C), RS1000364766 (14:66491945 G>A), RS1000648865 (14:66493823 T>C), RS1000793940 (14:66484661 C>G,T), RS1000833112 (14:66495755 T>A), RS1000947327 (14:66495496 T>C), RS1001330002 (14:66486438 C>G,T), RS1001545652 (14:66497835 A>G,T), RS1001651768 (14:66492632 G>A), RS1001725120 (14:66490979 C>A), RS1001836579 (14:66494075 T>C,G), RS1001952874 (14:66493689 T>C), RS1002225684 (14:66498096 T>C,G), RS1002605581 (14:66490170 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
GCST011639_6	Cirrhosis (alcohol related)	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	increases phosphorylation	1
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Endosulfan	increases expression	1
Silicon Dioxide	decreases expression	1
Valproic Acid	decreases methylation	1
Propofol	affects expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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