CCDC144A

Summary

CCDC144A (coiled-coil domain containing 144A, HGNC:29072) is a protein-coding gene on chromosome 17p11.2, encoding Coiled-coil domain-containing protein 144A (A2RUR9). May play a role in preventing the formation of kidney stones through inhibition of calcium oxalate monohydrate (COM) crystallization, attenuating COM-induced apoptotic injury to renal epithelial cells.

Predicted to enable calcium oxalate binding activity.

Source: NCBI Gene 9720 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 171 total
• MANE Select transcript: NM_001382000

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29072
Approved symbol	CCDC144A
Name	coiled-coil domain containing 144A
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0565, FLJ43983
Ensembl gene	ENSG00000170160
Ensembl biotype	protein_coding
OMIM	619413
Entrez	9720

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 6 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000328495, ENST00000340621, ENST00000360495, ENST00000360524, ENST00000399264, ENST00000399273, ENST00000420937, ENST00000428950, ENST00000436374, ENST00000463809, ENST00000470068, ENST00000478303, ENST00000697416, ENST00000904766

RefSeq mRNA: 2 — MANE Select: NM_001382000 NM_001382000, NM_014695

CCDS: CCDS45621, CCDS92264

Canonical transcript exons

ENST00000399273 — 17 exons

Exon	Start	End
ENSE00001537279	16773497	16777881
ENSE00003465339	16761425	16761718
ENSE00003480553	16732538	16732666
ENSE00003503749	16692979	16693049
ENSE00003510395	16690241	16690744
ENSE00003544694	16762313	16762533
ENSE00003576797	16727527	16727740
ENSE00003598575	16720198	16720231
ENSE00003626909	16711679	16711815
ENSE00003634995	16705151	16705399
ENSE00003646276	16763965	16764175
ENSE00003652711	16708796	16709635
ENSE00003658727	16720517	16720658
ENSE00003667963	16734690	16735643
ENSE00003686940	16731800	16731983
ENSE00003690880	16707469	16707542
ENSE00003693619	16771977	16772019

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 93.57.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1013 / max 87.0594, expressed in 456 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159715	1.1013	456

Top tissues by expression

262 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	93.57	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.52	gold quality
sural nerve	UBERON:0015488	79.00	gold quality
bone marrow cell	CL:0002092	78.78	gold quality
calcaneal tendon	UBERON:0003701	78.00	gold quality
colonic epithelium	UBERON:0000397	77.73	gold quality
right hemisphere of cerebellum	UBERON:0014890	76.81	gold quality
corpus callosum	UBERON:0002336	73.85	gold quality
right lung	UBERON:0002167	73.22	gold quality
adrenal tissue	UBERON:0018303	73.04	gold quality
cortical plate	UBERON:0005343	72.39	gold quality
testis	UBERON:0000473	72.25	gold quality
left testis	UBERON:0004533	71.21	gold quality
cerebellar hemisphere	UBERON:0002245	71.17	gold quality
cerebellar cortex	UBERON:0002129	71.06	gold quality
right testis	UBERON:0004534	70.54	gold quality
cerebellum	UBERON:0002037	68.66	gold quality
ventricular zone	UBERON:0003053	68.62	gold quality
right frontal lobe	UBERON:0002810	67.78	gold quality
body of pancreas	UBERON:0001150	67.55	gold quality
smooth muscle tissue	UBERON:0001135	67.12	gold quality
body of uterus	UBERON:0009853	67.04	gold quality
descending thoracic aorta	UBERON:0002345	66.47	gold quality
ganglionic eminence	UBERON:0004023	66.10	gold quality
right coronary artery	UBERON:0001625	66.02	gold quality
ascending aorta	UBERON:0001496	65.58	gold quality
thoracic aorta	UBERON:0001515	65.51	gold quality
monocyte	CL:0000576	65.39	gold quality
left coronary artery	UBERON:0001626	65.27	gold quality
popliteal artery	UBERON:0002250	65.25	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.13
E-MTAB-6678	yes	4.19
E-HCAD-31	no	2.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting CCDC144A, 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-3646	100.00	73.56	5283
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-204-5P	99.79	71.62	2439

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Coiled-coil domain-containing protein 144A — A2RUR9 (reviewed: A2RUR9)

All UniProt accessions (6): A2RUR9, A0A8V8TL21, A6NG92, A6NJB5, C9JAY6, C9JT67

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in preventing the formation of kidney stones through inhibition of calcium oxalate monohydrate (COM) crystallization, attenuating COM-induced apoptotic injury to renal epithelial cells. May exhibit antilithiatic (preventing the formation of kidney stones) activity through crystal binding, hindering the crystal attachment to renal epithelial cells, a pre-requisite to initiate inflammatory response.

Similarity. Belongs to the CCDC144 family.

Isoforms (3)

UniProt ID	Names	Canonical?
A2RUR9-1	1	yes
A2RUR9-2	2
A2RUR9-3	3

RefSeq proteins (2): NP_001368929, NP_055510 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021885	DUF3496	Domain
IPR039497	CC144C-like_CC_dom	Domain
IPR040118	C144A/B/C	Family

Pfam: PF12001, PF14915

UniProt features (23 total): compositionally biased region 8, region of interest 5, splice variant 5, coiled-coil region 3, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2RUR9-F1	61.65	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): GOMF_ORGANIC_ACID_BINDING, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, KMT2D_TARGET_GENES, ZNF184_TARGET_GENES, ZNF445_TARGET_GENES, ZNF592_TARGET_GENES, MIR3646, MIR4659A_3P_MIR4659B_3P, MIR204_5P, MIR211_5P, MIR568, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_DN, MIR6513_3P, MIR4436B_5P, MIR3974

GO Biological Process (0):

GO Molecular Function (1): calcium oxalate binding (GO:0046904)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
carboxylic acid binding	1

Protein interactions and networks

STRING

1427 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC144A	CDRT15L2	A8MXV6	599
CCDC144A	TBC1D28	Q2M2D7	583
CCDC144A	ZNF654	Q8IZM8	512
CCDC144A	SLC35G3	Q8N808	507
CCDC144A	SLC35G6	P0C7Q6	507
CCDC144A	CHCT1	Q86WR6	496
CCDC144A	SPDYE4	A6NLX3	480
CCDC144A	OR3A2	P47893	480
CCDC144A	TBC1D3G	Q6DHY5	479
CCDC144A	TBC1D26	Q86UD7	479
CCDC144A	TBC1D3B	A6NDS4	452
CCDC144A	LRRC3C	A6NJW4	450
CCDC144A	FBXW10B	O95170	447
CCDC144A	TMEM95	Q3KNT9	447
CCDC144A	A0A087WT91	A0A087WT91	446

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RAB28	CCDC144A	psi-mi:“MI:0914”(association)	0.510
RAB28	CCDC144A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): CCDC144A (Two-hybrid), CCDC144A (Affinity Capture-MS), CCDC144A (Negative Genetic), CCDC144A (Cross-Linking-MS (XL-MS)), CCDC144A (Cross-Linking-MS (XL-MS)), PRPF6 (Cross-Linking-MS (XL-MS)), CCDC144A (Affinity Capture-MS)

ESM2 similar proteins: A0A0A6YYL3, A0JP26, A2A2Z9, A2RUR9, A6NC57, A6NI47, A6QR20, A8MYB1, A9JSR5, A9ZSY0, B2RU33, B7ZQJ9, F1M5M3, H3BUK9, O15050, P51954, P98182, Q19UN5, Q4UJ75, Q501X2, Q5CZ79, Q5DW34, Q5SQ80, Q5TYW2, Q5VUR7, Q66HB6, Q6NSI1, Q6S545, Q6S5H5, Q6S8J7, Q71S21, Q7TPV2, Q7TSC3, Q7ZT11, Q80X59, Q811D2, Q86Y13, Q86YR6, Q8IVF6, Q8IYA2

Diamond homologs: A0A0A6YYL3, A0JP26, A0PJZ0, A2A2Z9, A2RUR9, A5A3E0, A6NC57, A6NI47, A7E2S9, B2RU33, H3BUK9, P0CG38, P0CG39, Q3MJ40, Q4R3S3, Q4UJ75, Q5CZ79, Q5JPF3, Q5SQ80, Q5TYW2, Q5VUR7, Q6NSI1, Q6S545, Q6S5H5, Q6S8J3, Q6S8J7, Q811D2, Q86YR6, Q8IYA2, Q92527, Q9BXX2, Q9BXX3, Q9D504, Q9H560, Q9UPS8, A6QL64, Q8IVF6, Q8N2N9, Q8NF67, Q96IX9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	137
Likely benign	24
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3083 predictions. Top by Δscore:

Variant	Effect	Δscore
17:16690736:G:GT	donor_gain	1.0000
17:16690742:GAG:G	donor_gain	1.0000
17:16692966:T:G	acceptor_gain	1.0000
17:16692974:CATA:C	acceptor_loss	1.0000
17:16692976:T:G	acceptor_gain	1.0000
17:16692976:TA:T	acceptor_loss	1.0000
17:16692976:TAGCA:T	acceptor_gain	1.0000
17:16692977:A:AG	acceptor_gain	1.0000
17:16692977:AG:A	acceptor_loss	1.0000
17:16692977:AGCAT:A	acceptor_loss	1.0000
17:16692978:G:GA	acceptor_gain	1.0000
17:16692978:G:GC	acceptor_gain	1.0000
17:16692978:GC:G	acceptor_gain	1.0000
17:16692978:GCA:G	acceptor_gain	1.0000
17:16692978:GCATT:G	acceptor_gain	1.0000
17:16693046:CCAGG:C	donor_loss	1.0000
17:16693047:CAGG:C	donor_loss	1.0000
17:16693048:AGG:A	donor_loss	1.0000
17:16693050:G:A	donor_loss	1.0000
17:16693050:G:GA	donor_loss	1.0000
17:16693051:T:A	donor_loss	1.0000
17:16705338:G:T	donor_gain	1.0000
17:16705396:GAAG:G	donor_gain	1.0000
17:16705397:AAGG:A	donor_loss	1.0000
17:16705398:AGGT:A	donor_loss	1.0000
17:16705398:AGGTA:A	donor_loss	1.0000
17:16705399:GGT:G	donor_loss	1.0000
17:16705400:G:A	donor_loss	1.0000
17:16705400:G:C	donor_loss	1.0000
17:16705401:T:A	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000010888 (17:16752353 A>G), RS1000041112 (17:16752576 C>G,T), RS1000147940 (17:16693396 A>G), RS1000201190 (17:16693567 G>A,T), RS1000212249 (17:16733488 T>C,G), RS1000217707 (17:16746174 C>G), RS1000370571 (17:16738432 C>T), RS1000394287 (17:16729587 C>G,T), RS1000399989 (17:16736206 A>T), RS1000410877 (17:16682214 T>A), RS1000425614 (17:16729194 A>G,T), RS1000456576 (17:16701619 T>A), RS1000591120 (17:16676616 A>G), RS1000604648 (17:16740003 G>T), RS1000646161 (17:16689443 C>T)

Disease associations

OMIM: gene MIM:619413 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
kojic acid	decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
arsenite	affects expression	1
sodium arsenite	decreases expression	1
aflatoxin B2	increases methylation	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	increases expression	1
Fulvestrant	decreases methylation	1
Air Pollutants	decreases expression	1
Arsenic	affects methylation	1
Catechin	increases expression, affects cotreatment	1
Silicon Dioxide	increases expression	1
Testosterone	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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