CCDC122

Summary

CCDC122 (coiled-coil domain containing 122, HGNC:26478) is a protein-coding gene on chromosome 13q14.11, encoding Coiled-coil domain-containing protein 122 (Q5T0U0).

This gene encodes a protein that contains a coiled-coil domain. Naturally occurring mutations in this gene are associated with leprosy.

Source: NCBI Gene 160857 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_144974

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26478
Approved symbol	CCDC122
Name	coiled-coil domain containing 122
Location	13q14.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31846
Ensembl gene	ENSG00000151773
Ensembl biotype	protein_coding
OMIM	613408
Entrez	160857

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000444614, ENST00000470137, ENST00000476570, ENST00000611737, ENST00000614023, ENST00000928435, ENST00000962404, ENST00000962405

RefSeq mRNA: 3 — MANE Select: NM_144974 NM_001350617, NM_001350618, NM_144974

CCDS: CCDS9390

Canonical transcript exons

ENST00000444614 — 7 exons

Exon	Start	End
ENSE00001480042	43874842	43874927
ENSE00001534684	43879631	43879740
ENSE00001751665	43836352	43837429
ENSE00003468291	43868694	43868803
ENSE00003524812	43869331	43869489
ENSE00003583863	43858781	43858897
ENSE00003634550	43859672	43860070

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 87.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.0647 / max 69.1408, expressed in 1539 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
137028	4.0053	1341
137027	0.8535	549
137026	0.7941	464
137025	0.3504	105
137024	0.0614	35

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	87.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.45	gold quality
body of pancreas	UBERON:0001150	81.44	gold quality
islet of Langerhans	UBERON:0000006	81.18	gold quality
rectum	UBERON:0001052	80.22	gold quality
pancreas	UBERON:0001264	79.68	gold quality
left lobe of thyroid gland	UBERON:0001120	79.65	gold quality
smooth muscle tissue	UBERON:0001135	79.57	gold quality
colonic epithelium	UBERON:0000397	79.55	gold quality
right lobe of thyroid gland	UBERON:0001119	78.91	gold quality
left ovary	UBERON:0002119	78.68	gold quality
right uterine tube	UBERON:0001302	78.62	gold quality
thyroid gland	UBERON:0002046	78.58	gold quality
right ovary	UBERON:0002118	78.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.98	gold quality
left adrenal gland cortex	UBERON:0035825	77.90	gold quality
left adrenal gland	UBERON:0001234	77.86	gold quality
right adrenal gland cortex	UBERON:0035827	77.69	gold quality
minor salivary gland	UBERON:0001830	77.64	gold quality
cortical plate	UBERON:0005343	77.60	gold quality
metanephros cortex	UBERON:0010533	77.41	gold quality
body of uterus	UBERON:0009853	77.30	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.28	gold quality
gall bladder	UBERON:0002110	77.20	gold quality
adrenal tissue	UBERON:0018303	77.08	gold quality
right coronary artery	UBERON:0001625	77.05	gold quality
right adrenal gland	UBERON:0001233	76.45	gold quality
endocervix	UBERON:0000458	76.11	gold quality
adrenal gland	UBERON:0002369	75.70	gold quality
left uterine tube	UBERON:0001303	75.68	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	639.53
E-ENAD-27	yes	318.54
E-ANND-3	yes	4.78
E-MTAB-6379	no	344.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting CCDC122, 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-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-6755-5P	99.95	65.59	464
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-3681-5P	99.82	66.88	387
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-6513-3P	99.59	69.77	1102
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-16-2-3P	99.29	70.60	1954
HSA-MIR-195-3P	99.29	70.61	1954
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-4477A	98.83	69.75	2952

Literature-anchored findings (GeneRIF, showing 2)

• the apparent occurrence of an unusual TG 3’ splice site in intron 7 (according to mRNA AK056408) is discussed (PMID:17672918)
• Association between leprosy and tag SNPs at NOD2 (rs8057431) and CCDC122-LACC1 (rs4942254). (PMID:25367361)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc122	ENSMUSG00000034795
rattus_norvegicus	Ccdc122	ENSRNOG00000042404
drosophila_melanogaster	SMC3	FBGN0015615
caenorhabditis_elegans		WBGENE00004873
caenorhabditis_elegans		WBGENE00012198
caenorhabditis_elegans		WBGENE00019087

Paralogs (7): SMC1A (ENSG00000072501), SMC1B (ENSG00000077935), SMC3 (ENSG00000108055), SMC4 (ENSG00000113810), CKAP4 (ENSG00000136026), SMC2 (ENSG00000136824), CCDC157 (ENSG00000187860)

Protein

Protein identifiers

Coiled-coil domain-containing protein 122 — Q5T0U0 (reviewed: Q5T0U0)

All UniProt accessions (2): Q5T0U0, A0A087WWN1

Isoforms (2)

UniProt ID	Names	Canonical?
Q5T0U0-1	1	yes
Q5T0U0-2	2

RefSeq proteins (3): NP_001337546, NP_001337547, NP_659411* (*=MANE)

Domains & families (InterPro)

UniProt features (7 total): coiled-coil region 2, chain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T0U0-F1	89.26	0.75

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 60 (showing top): chr13q14, YATGNWAAT_OCT_C, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP, MEISSNER_NPC_HCP_WITH_H3K4ME2, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_UP, CREB3L4_TARGET_GENES, HAND1_TARGET_GENES, PAX3_TARGET_GENES, RYBP_TARGET_GENES, ZNF213_TARGET_GENES, ZNF592_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC122	LACC1	Q8IV20	945
CCDC122	TNFSF15	O95150	779
CCDC122	RIPK2	O43353	749
CCDC122	LRRK2	Q5S007	720
CCDC122	NOD2	Q9HC29	704
CCDC122	SPRYD7	Q5W111	631
CCDC122	PACRG	Q96M98	583
CCDC122	VIL1	P09327	543
CCDC122	SLC11A1	P49279	537
CCDC122	PRKN	O60260	519
CCDC122	TLR1	Q15399	511
CCDC122	CCDC137	Q6PK04	508
CCDC122	TNP1	P09430	497
CCDC122	LTA4H	P09960	494
CCDC122	Q5Y7H0	Q5Y7H0	469

IntAct

13 interactions, top by confidence:

A	B	Type	Score
CCDC172	EPS15	psi-mi:“MI:0914”(association)	0.530
BORCS6	HSBP1	psi-mi:“MI:0914”(association)	0.530
FAM167A	SHTN1	psi-mi:“MI:0914”(association)	0.350
S100A2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SYCE1	RABGAP1L	psi-mi:“MI:0914”(association)	0.350
BORCS6	UQCRQ	psi-mi:“MI:0914”(association)	0.350
TFPT	CCDC122	psi-mi:“MI:0915”(physical association)	0.000
NCKAP5L	CCDC122	psi-mi:“MI:0915”(physical association)	0.000
CCDC122	PKN3	psi-mi:“MI:0915”(physical association)	0.000
	CCDC122	psi-mi:“MI:0915”(physical association)	0.000
CCDC122	recN	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), PKN3 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (Affinity Capture-MS), CCDC122 (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: Q5T0U0, Q8BVN0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1222 predictions. Top by Δscore:

Variant	Effect	Δscore
13:43858912:CATT:C	acceptor_gain	1.0000
13:43858915:T:C	acceptor_gain	1.0000
13:43858915:T:TC	acceptor_gain	1.0000
13:43858920:A:AC	acceptor_gain	1.0000
13:43858922:A:C	acceptor_gain	1.0000
13:43874888:T:TA	donor_gain	1.0000
13:43878780:AAGT:A	donor_gain	1.0000
13:43858913:A:C	acceptor_gain	0.9900
13:43858920:A:C	acceptor_gain	0.9900
13:43858922:A:AC	acceptor_gain	0.9900
13:43868810:T:TC	acceptor_gain	0.9900
13:43874844:A:AC	donor_gain	0.9900
13:43874928:C:CC	acceptor_gain	0.9900
13:43879370:T:TA	donor_gain	0.9900
13:43879428:C:CA	donor_gain	0.9900
13:43879458:T:TA	donor_gain	0.9900
13:43879464:T:A	donor_gain	0.9900
13:43879732:GAGG:G	donor_loss	0.9900
13:43879734:GG:G	donor_loss	0.9900
13:43879735:G:GA	donor_loss	0.9900
13:43837426:GTAC:G	acceptor_loss	0.9800
13:43837430:C:G	acceptor_loss	0.9800
13:43858774:GACTT:G	donor_loss	0.9800
13:43858775:ACTT:A	donor_loss	0.9800
13:43858776:CTTAC:C	donor_loss	0.9800
13:43858777:TTACC:T	donor_loss	0.9800
13:43858778:TACC:T	donor_loss	0.9800
13:43858779:A:T	donor_loss	0.9800
13:43858780:C:T	donor_loss	0.9800
13:43860067:CATT:C	acceptor_gain	0.9800

AlphaMissense

1840 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:43837408:C:G	A232P	0.944
13:43837415:C:A	R229S	0.941
13:43837415:C:G	R229S	0.941
13:43837395:C:G	R236P	0.940
13:43837407:G:T	A232E	0.925
13:43837396:G:T	R236S	0.922
13:43837401:A:G	L234P	0.922
13:43837418:C:A	K228N	0.922
13:43837418:C:G	K228N	0.922
13:43837356:C:G	R249P	0.892
13:43837392:A:G	L237S	0.880
13:43859907:A:G	L107P	0.879
13:43837397:C:A	K235N	0.858
13:43837397:C:G	K235N	0.858
13:43837318:C:G	A262P	0.856
13:43859721:A:G	L169P	0.844
13:43868759:C:G	A31P	0.834
13:43837416:C:G	R229T	0.814
13:43859949:A:G	L93P	0.804
13:43837416:C:A	R229M	0.786
13:43859772:A:G	L152P	0.782
13:43860063:A:G	L55P	0.781
13:43837417:T:C	R229G	0.775
13:43837396:G:C	R236G	0.774
13:43859887:C:G	A114P	0.767
13:43837383:T:G	Q240P	0.764
13:43837419:T:G	K228T	0.761
13:43860054:A:G	L58P	0.755
13:43837420:T:C	K228E	0.750
13:43837371:A:G	L244P	0.745

dbSNP variants (sampled 300 via entrez): RS1000144778 (13:43854931 C>G), RS1000225338 (13:43857977 T>C), RS1000296455 (13:43848386 T>A,C), RS1000316463 (13:43852915 T>A,C), RS1000340031 (13:43868488 A>G), RS1000350601 (13:43848647 T>C), RS1000387078 (13:43846340 T>C), RS1000399419 (13:43839325 T>C), RS1000429943 (13:43859143 G>A), RS1000563866 (13:43835910 G>A,C), RS1000592817 (13:43871462 T>C), RS1000600331 (13:43855240 C>A), RS1000660774 (13:43840943 C>T), RS1000786716 (13:43828014 G>A), RS1000830280 (13:43840998 T>A,C)

Disease associations

OMIM: gene MIM:613408 | disease phenotypes: MIM:609888, MIM:618795

GenCC curated gene-disease

Mondo (2): leprosy, susceptibility to, 1 (MONDO:0012358), juvenile arthritis due to defect in LACC1 (MONDO:0032920)

Orphanet (1): Leprosy (Orphanet:548)

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004131_66	Inflammatory bowel disease	3.000000e-08
GCST004132_108	Crohn’s disease	1.000000e-13
GCST005839_43	Depression	3.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases methylation	1
sodium arsenite	increases expression	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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