CCDC73

Summary

CCDC73 (coiled-coil domain containing 73, HGNC:23261) is a protein-coding gene on chromosome 11p13, encoding Coiled-coil domain-containing protein 73 (Q6ZRK6).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 149 total
• MANE Select transcript: NM_001008391

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23261
Approved symbol	CCDC73
Name	coiled-coil domain containing 73
Location	11p13
Locus type	gene with protein product
Status	Approved
Aliases	NY-SAR-79
Ensembl gene	ENSG00000186714
Ensembl biotype	protein_coding
OMIM	612328
Entrez	493860

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000335185, ENST00000528333, ENST00000531481, ENST00000534415

RefSeq mRNA: 1 — MANE Select: NM_001008391 NM_001008391

CCDS: CCDS41630

Canonical transcript exons

ENST00000335185 — 18 exons

Exon	Start	End
ENSE00001331900	32613422	32614942
ENSE00001371373	32602721	32603020
ENSE00001387093	32611132	32611265
ENSE00001390585	32615940	32616129
ENSE00001402469	32794613	32794662
ENSE00001424542	32653123	32653227
ENSE00003499831	32760109	32760258
ENSE00003534148	32675565	32675644
ENSE00003544538	32718076	32718147
ENSE00003555364	32635696	32635830
ENSE00003568048	32653978	32654037
ENSE00003598152	32700791	32700826
ENSE00003615919	32654844	32654972
ENSE00003626943	32641972	32642082
ENSE00003670630	32702873	32702944
ENSE00003677811	32699251	32699325
ENSE00003680335	32675886	32676021
ENSE00003686714	32683536	32683574

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 87.71.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0081 / max 6.3152, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119190	0.0081	4

Top tissues by expression

134 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	87.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.46	gold quality
testis	UBERON:0000473	67.72	gold quality
right testis	UBERON:0004534	67.31	gold quality
ventricular zone	UBERON:0003053	66.31	gold quality
cortical plate	UBERON:0005343	66.05	gold quality
left testis	UBERON:0004533	65.18	gold quality
calcaneal tendon	UBERON:0003701	64.76	gold quality
corpus callosum	UBERON:0002336	61.19	gold quality
adrenal tissue	UBERON:0018303	60.60	gold quality
monocyte	CL:0000576	60.22	gold quality
leukocyte	CL:0000738	60.18	gold quality
right lobe of liver	UBERON:0001114	59.44	gold quality
liver	UBERON:0002107	58.52	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	56.93	gold quality
ganglionic eminence	UBERON:0004023	55.95	gold quality
stromal cell of endometrium	CL:0002255	55.65	gold quality
endometrium	UBERON:0001295	54.96	gold quality
granulocyte	CL:0000094	52.90	gold quality
left ovary	UBERON:0002119	52.35	gold quality
ovary	UBERON:0000992	51.97	gold quality
bone marrow	UBERON:0002371	51.95	silver quality
spleen	UBERON:0002106	51.83	gold quality
prefrontal cortex	UBERON:0000451	51.00	gold quality
right uterine tube	UBERON:0001302	50.28	gold quality
right ovary	UBERON:0002118	49.86	gold quality
lymph node	UBERON:0000029	49.60	gold quality
cerebellar hemisphere	UBERON:0002245	49.55	silver quality
lower esophagus mucosa	UBERON:0035834	49.51	gold quality
cerebellar cortex	UBERON:0002129	49.47	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting CCDC73, 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-5692A	100.00	74.40	6850
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3185	99.99	68.12	1959
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-26A-1-3P	99.64	66.81	788
HSA-MIR-26A-2-3P	99.64	66.82	786
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-425-5P	99.59	67.67	900
HSA-MIR-4762-5P	99.57	68.54	1424

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc73	ENSDARG00000093805
mus_musculus	Ccdc73	ENSMUSG00000045106
rattus_norvegicus	Ccdc73	ENSRNOG00000022660

Protein

Protein identifiers

Coiled-coil domain-containing protein 73 — Q6ZRK6 (reviewed: Q6ZRK6)

Alternative names: Sarcoma antigen NY-SAR-79

All UniProt accessions (3): A6H8Y7, Q6ZRK6, H0YDV2

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZRK6-1	1	yes
Q6ZRK6-2	2

RefSeq proteins (1): NP_001008392* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031650	CCDC73	Family

Pfam: PF15818

UniProt features (9 total): splice variant 3, coiled-coil region 2, chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZRK6-F1	54.16	0.20

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): HMGA1_TARGET_GENES, MAFG_TARGET_GENES, ZNF274_TARGET_GENES, ZNF512_TARGET_GENES, MIR548AJ_3P_MIR548X_3P, MIR548AE_3P_MIR548AQ_3P, MIR548AH_3P_MIR548AM_3P, MIR548J_3P, MIR4261, MIR4799_5P, MIR147B_5P, MIR4677_5P, MIR372_5P, MIR4768_3P, MIR548AO_5P_MIR548AX

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

484 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC73	CTAG1A	P78358	829
CCDC73	TCP11L1	Q9NUJ3	645
CCDC73	QSER1	Q2KHR3	612
CCDC73	PRRG4	Q9BZD6	605
CCDC73	DCDC1	P59894	579
CCDC73	EIF3M	Q7L2H7	576
CCDC73	Q6NXN5	Q6NXN5	570
CCDC73	CDCP2	Q5VXM1	561
CCDC73	DEPDC7	Q96QD5	556
CCDC73	PTPDC1	A2A3K4	534
CCDC73	KANK3	Q6NY19	525
CCDC73	PRR19	A6NJB7	497
CCDC73	KLK9	Q9UKQ9	492
CCDC73	C3orf70	A6NLC5	480
CCDC73	CSTF3	Q12996	460

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CCDC73		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): CCDC73 (Affinity Capture-MS), CCDC73 (Affinity Capture-MS), CCDC73 (Protein-RNA), CCDC73 (Cross-Linking-MS (XL-MS)), CCDC73 (Cross-Linking-MS (XL-MS)), C6orf211 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0P8Z5, A2AM05, A2RUB6, A7E3D8, A8MT70, B0CM36, B1WC58, E9PVD1, F6SNN2, O35618, O75410, O95447, Q3UPP8, Q3V036, Q4KMA0, Q4R3Q7, Q5PQS2, Q5R9L2, Q5RBD6, Q5U5Q9, Q5VVM6, Q5VX52, Q5VXU9, Q5W0Q7, Q6NRH3, Q6NZK5, Q6P7W0, Q6P9F0, Q6PJW8, Q6Y685, Q6ZRK6, Q70YC5, Q7Z4H7, Q86T90, Q86Z20, Q8BFU3, Q8BG89, Q8BVF4, Q8CDM4, Q8IW35

Diamond homologs: Q6ZRK6, Q8CDM4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	120
Likely benign	18
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3225 predictions. Top by Δscore:

Variant	Effect	Δscore
11:32611130:A:AC	donor_gain	1.0000
11:32611131:C:CC	donor_gain	1.0000
11:32615951:ATTT:A	donor_gain	1.0000
11:32615954:T:A	donor_gain	1.0000
11:32635712:T:TA	donor_gain	1.0000
11:32641965:AACTT:A	donor_loss	1.0000
11:32641966:ACTTA:A	donor_loss	1.0000
11:32641967:CTTA:C	donor_loss	1.0000
11:32641968:T:TC	donor_loss	1.0000
11:32641969:T:TG	donor_loss	1.0000
11:32641970:A:AC	donor_gain	1.0000
11:32641970:A:C	donor_loss	1.0000
11:32641971:C:CC	donor_gain	1.0000
11:32641971:C:T	donor_loss	1.0000
11:32641971:CAT:C	donor_gain	1.0000
11:32641971:CATGT:C	donor_gain	1.0000
11:32653118:CGAA:C	donor_loss	1.0000
11:32653121:AC:A	donor_loss	1.0000
11:32653122:C:A	donor_loss	1.0000
11:32653204:A:C	acceptor_gain	1.0000
11:32653207:T:TC	acceptor_gain	1.0000
11:32653227:CCTT:C	acceptor_gain	1.0000
11:32653227:CCTTT:C	acceptor_loss	1.0000
11:32653228:C:CC	acceptor_gain	1.0000
11:32653228:CTTTG:C	acceptor_loss	1.0000
11:32653229:T:C	acceptor_gain	1.0000
11:32653230:T:C	acceptor_gain	1.0000
11:32653230:T:TC	acceptor_gain	1.0000
11:32675645:C:CC	acceptor_gain	1.0000
11:32675652:A:C	acceptor_gain	1.0000

AlphaMissense

7277 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:32675636:C:G	A192P	0.994
11:32699255:A:G	L129P	0.981
11:32642015:A:G	L336P	0.979
11:32654968:A:G	L217P	0.979
11:32760119:C:G	R42P	0.979
11:32760135:C:G	A37P	0.978
11:32718089:A:G	L65P	0.976
11:32642060:A:G	L321P	0.975
11:32675969:A:G	L161P	0.971
11:32675614:A:G	L199P	0.967
11:32702896:C:G	A86P	0.964
11:32654863:A:G	L252P	0.957
11:32675994:C:G	A153P	0.950
11:32675593:T:G	Q206P	0.949
11:32760122:A:G	L41S	0.948
11:32760109:C:A	R45S	0.945
11:32760109:C:G	R45S	0.945
11:32675906:T:G	H182P	0.944
11:32702937:A:G	L72P	0.944
11:32683571:A:G	S132P	0.943
11:32675926:A:C	F175L	0.941
11:32675926:A:T	F175L	0.941
11:32675928:A:G	F175L	0.941
11:32718080:T:G	Q68P	0.941
11:32718144:C:G	A47P	0.940
11:32654939:A:G	S227P	0.930
11:32641995:C:G	A343P	0.927
11:32642023:A:C	F333L	0.927
11:32642023:A:T	F333L	0.927
11:32642025:A:G	F333L	0.927

dbSNP variants (sampled 300 via entrez): RS1000010601 (11:32699547 G>A), RS1000016157 (11:32754666 T>A), RS1000017024 (11:32737966 C>T), RS1000068152 (11:32831198 T>C), RS1000075575 (11:32732667 T>G), RS1000075868 (11:32614305 T>A,C), RS1000116775 (11:32775101 G>A), RS1000138333 (11:32823931 G>A,T), RS1000139300 (11:32738337 T>C,G), RS1000146504 (11:32661363 C>G,T), RS1000170386 (11:32647531 A>T), RS1000174710 (11:32795523 A>C), RS1000179501 (11:32675464 C>A,T), RS1000190322 (11:32640021 T>A,G), RS1000212721 (11:32802005 TGA>T)

Disease associations

OMIM: gene MIM:612328 | 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
GCST009391_1794	Metabolite levels	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010449	3-methyladipic acid measurement
EFO:0010524	pimelic acid measurement

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
sodium arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	decreases methylation	1
jinfukang	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Methapyrilene	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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