CCDC90B

Summary

CCDC90B (coiled-coil domain containing 90B, HGNC:28108) is a protein-coding gene on chromosome 11q14.1, encoding Coiled-coil domain-containing protein 90B, mitochondrial (Q9GZT6).

Located in mitochondrion.

Source: NCBI Gene 60492 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 57 total
• MANE Select transcript: NM_021825

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28108
Approved symbol	CCDC90B
Name	coiled-coil domain containing 90B
Location	11q14.1
Locus type	gene with protein product
Status	Approved
Aliases	MDS025, MDS011
Ensembl gene	ENSG00000137500
Ensembl biotype	protein_coding
OMIM	620753
Entrez	60492

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 10 nonsense_mediated_decay, 10 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000260054, ENST00000455220, ENST00000525503, ENST00000525504, ENST00000525916, ENST00000526265, ENST00000526631, ENST00000527025, ENST00000527495, ENST00000528149, ENST00000529073, ENST00000529312, ENST00000529611, ENST00000529689, ENST00000529745, ENST00000529856, ENST00000530253, ENST00000533761, ENST00000534753, ENST00000874525, ENST00000874526, ENST00000874527, ENST00000874528, ENST00000915430, ENST00000915431

RefSeq mRNA: 6 — MANE Select: NM_021825 NM_001286116, NM_001286117, NM_001286118, NM_001286119, NM_001286120, NM_021825

CCDS: CCDS66190, CCDS8266

Canonical transcript exons

ENST00000529689 — 9 exons

Exon	Start	End
ENSE00002144130	83259081	83261966
ENSE00002197186	83285873	83286367
ENSE00003492257	83273951	83273992
ENSE00003542415	83265865	83265979
ENSE00003551859	83278726	83278829
ENSE00003573079	83274639	83274740
ENSE00003574461	83273647	83273700
ENSE00003674065	83273793	83273864
ENSE00003684979	83280141	83280260

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 97.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.7169 / max 775.5929, expressed in 1819 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
121599	28.0208	1807
121602	8.3502	1786
121597	2.3976	1241
121601	2.1183	1347
121598	1.2846	873
121600	0.5062	269
121596	0.3917	185
121603	0.3705	152
121595	0.2768	124

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	97.89	gold quality
ganglionic eminence	UBERON:0004023	97.16	gold quality
ventricular zone	UBERON:0003053	97.08	gold quality
adrenal tissue	UBERON:0018303	97.01	gold quality
calcaneal tendon	UBERON:0003701	96.92	gold quality
sperm	CL:0000019	96.53	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.35	gold quality
left testis	UBERON:0004533	96.26	gold quality
right testis	UBERON:0004534	96.18	gold quality
spinal cord	UBERON:0002240	95.98	gold quality
corpus callosum	UBERON:0002336	95.94	gold quality
male germ cell	CL:0000015	95.77	gold quality
testis	UBERON:0000473	95.64	gold quality
right adrenal gland cortex	UBERON:0035827	95.59	gold quality
tendon	UBERON:0000043	95.45	gold quality
right adrenal gland	UBERON:0001233	95.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	95.05	gold quality
left adrenal gland	UBERON:0001234	94.80	gold quality
right coronary artery	UBERON:0001625	94.80	gold quality
adrenal gland	UBERON:0002369	94.78	gold quality
adrenal cortex	UBERON:0001235	94.53	gold quality
left adrenal gland cortex	UBERON:0035825	94.50	gold quality
endothelial cell	CL:0000115	94.43	gold quality
embryo	UBERON:0000922	94.42	gold quality
islet of Langerhans	UBERON:0000006	94.36	gold quality
amniotic fluid	UBERON:0000173	94.28	gold quality
tibia	UBERON:0000979	93.98	gold quality
left coronary artery	UBERON:0001626	93.45	gold quality
tendon of biceps brachii	UBERON:0008188	93.43	gold quality
substantia nigra	UBERON:0002038	93.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

97 targeting CCDC90B, 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-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646

Literature-anchored findings (GeneRIF, showing 1)

• Using MCUR1, the functionally characterized paralog of study the role of individual domains, results find that the conserved head domain in CCDC90B interacts directly with mitochondrial calcium uniporter and is destabilized upon Ca(2+) binding. (PMID:30612859)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc90b	ENSDARG00000044626
mus_musculus	Ccdc90b	ENSMUSG00000030613
rattus_norvegicus	Ccdc90b	ENSRNOG00000009462

Paralogs (1): MCUR1 (ENSG00000050393)

Protein

Protein identifiers

Coiled-coil domain-containing protein 90B, mitochondrial — Q9GZT6 (reviewed: Q9GZT6)

All UniProt accessions (10): Q9GZT6, E9PKQ5, E9PMQ7, E9PNI8, E9PPJ7, E9PRC2, E9PSG6, H0YD95, H0YF06, J3KN19

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with MCU.

Subcellular location. Mitochondrion membrane.

Similarity. Belongs to the CCDC90 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9GZT6-1	1	yes
Q9GZT6-2	2
Q9GZT6-3	3

RefSeq proteins (6): NP_001273045, NP_001273046, NP_001273047, NP_001273048, NP_001273049, NP_068597* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024461	CCDC90-like	Family

Pfam: PF07798

UniProt features (11 total): helix 3, splice variant 2, transit peptide 1, chain 1, transmembrane region 1, coiled-coil region 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6H9M	X-RAY DIFFRACTION	2.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9GZT6-F1	81.37	0.63

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 121 (showing top): MODULE_255, MODULE_317, AACYNNNNTTCCS_UNKNOWN, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOCC_MITOCHONDRIAL_ENVELOPE, ZHANG_BREAST_CANCER_PROGENITORS_UP, BERNARD_PPAPDC1B_TARGETS_UP, LEE_LIVER_CANCER_E2F1_DN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4, NUYTTEN_EZH2_TARGETS_DN, MODULE_69, RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN, GOCC_ORGANELLE_ENVELOPE, BRUINS_UVC_RESPONSE_LATE, MODULE_37

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial membrane (GO:0031966), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
mitochondrial envelope	1
organelle membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

486 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC90B	FAM32A	Q9Y421	592
CCDC90B	NIPAL2	Q9H841	566
CCDC90B	TRMT1L	Q7Z2T5	557
CCDC90B	ANKRD42	Q8N9B4	534
CCDC90B	MRPL53	Q96EL3	517
CCDC90B	WDR74	Q6RFH5	495
CCDC90B	IGSF22	Q8N9C0	487
CCDC90B	RAB30	Q15771	476
CCDC90B	CXorf65	A6NEN9	473
CCDC90B	SMCO2	A6NFE2	471
CCDC90B	MICU1	Q9BPX6	466
CCDC90B	LRRC66	Q68CR7	458
CCDC90B	NOB1	Q9ULX3	457
CCDC90B	TMX1	Q9H3N1	456
CCDC90B	C11orf52	Q96A22	446

IntAct

63 interactions, top by confidence:

A	B	Type	Score
MOB2	CCDC90B	psi-mi:“MI:0915”(physical association)	0.560
CCDC90B	GORASP2	psi-mi:“MI:0915”(physical association)	0.560
CCDC90B	YWHAG	psi-mi:“MI:0915”(physical association)	0.560
CCDC90B	SETDB1	psi-mi:“MI:0915”(physical association)	0.560
KAT5	CCDC90B	psi-mi:“MI:0915”(physical association)	0.560
LMO3	CCDC90B	psi-mi:“MI:0915”(physical association)	0.560
CCDC90B	MCUR1	psi-mi:“MI:0915”(physical association)	0.560
MCUR1	CCDC90B	psi-mi:“MI:0915”(physical association)	0.560
CCDC90B	TK1	psi-mi:“MI:0915”(physical association)	0.550
TSC22D1	CCDC90B	psi-mi:“MI:0915”(physical association)	0.550
CTSV	CCDC90B	psi-mi:“MI:0915”(physical association)	0.400
CCDC90B		psi-mi:“MI:0915”(physical association)	0.370
CCDC90B	ANXA7	psi-mi:“MI:0915”(physical association)	0.370
DNM2	CCDC90B	psi-mi:“MI:0915”(physical association)	0.370
NIPSNAP3A	CCDC90B	psi-mi:“MI:0915”(physical association)	0.370
PIN1	CCDC90B	psi-mi:“MI:0915”(physical association)	0.370
SMN1	CCDC90B	psi-mi:“MI:0915”(physical association)	0.370
HSPA4	HSPA8	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC25A16	TOMM70	psi-mi:“MI:0914”(association)	0.350

BioGRID (230): MCUR1 (Affinity Capture-MS), MCUR1 (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS), CCDC90B (Synthetic Lethality), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid), CCDC90B (Two-hybrid)

ESM2 similar proteins: A4QP73, A5DAI1, A8X0L4, A8XDF8, A9UQS1, B4IK33, E5KGE0, F4I111, O14042, O42997, O60065, O74552, O74925, O80996, O94308, O94689, P43557, P87150, Q05867, Q09743, Q09777, Q10073, Q10410, Q19954, Q21121, Q22505, Q23679, Q3SZ76, Q4V897, Q54LT0, Q618H8, Q626S1, Q6CTB6, Q6DJ87, Q6FIK2, Q6S5G3, Q751P7, Q8C3X2, Q8S9K7, Q8SYD0

Diamond homologs: Q0P4J6, Q4V897, Q6DJ87, Q8C3X2, Q96AQ8, Q9CXD6, Q9GZT6, Q10073

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1169 predictions. Top by Δscore:

Variant	Effect	Δscore
11:83273642:TTTAC:T	donor_loss	1.0000
11:83273643:TTA:T	donor_loss	1.0000
11:83273645:A:AT	donor_loss	1.0000
11:83273646:C:CG	donor_loss	1.0000
11:83273701:C:CC	acceptor_gain	1.0000
11:83273787:CATTA:C	donor_loss	1.0000
11:83273788:ATTAC:A	donor_loss	1.0000
11:83273789:TTACC:T	donor_loss	1.0000
11:83273790:TAC:T	donor_loss	1.0000
11:83273791:A:T	donor_loss	1.0000
11:83273792:C:CA	donor_loss	1.0000
11:83273797:T:C	donor_gain	1.0000
11:83273861:CATG:C	acceptor_gain	1.0000
11:83273865:C:CC	acceptor_gain	1.0000
11:83273866:T:C	acceptor_gain	1.0000
11:83273993:C:CC	acceptor_gain	1.0000
11:83274635:TCACC:T	donor_loss	1.0000
11:83274636:CAC:C	donor_loss	1.0000
11:83274638:CC:C	donor_loss	1.0000
11:83274640:T:TA	donor_gain	1.0000
11:83274695:T:A	donor_gain	1.0000
11:83274737:TTTC:T	acceptor_gain	1.0000
11:83274738:TTC:T	acceptor_gain	1.0000
11:83274739:TC:T	acceptor_gain	1.0000
11:83274740:CC:C	acceptor_gain	1.0000
11:83274741:C:CC	acceptor_gain	1.0000
11:83274741:CTAGA:C	acceptor_loss	1.0000
11:83274742:T:C	acceptor_loss	1.0000
11:83280083:A:C	donor_gain	1.0000
11:83280189:T:A	donor_gain	1.0000

AlphaMissense

1682 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:83274663:A:C	F134L	0.996
11:83274663:A:T	F134L	0.996
11:83274665:A:G	F134L	0.996
11:83261952:A:G	C242R	0.993
11:83274655:A:G	L137P	0.991
11:83278812:C:G	A80P	0.988
11:83261933:C:T	G248E	0.987
11:83261942:A:T	I245K	0.985
11:83265867:G:T	A236E	0.985
11:83274679:A:G	L129P	0.983
11:83265898:A:G	S226P	0.982
11:83261934:C:G	G248R	0.981
11:83261934:C:T	G248R	0.981
11:83273955:A:G	L155P	0.980
11:83274669:A:C	S132R	0.980
11:83274669:A:T	S132R	0.980
11:83274671:T:G	S132R	0.980
11:83261945:G:T	A244E	0.979
11:83274694:T:A	K124I	0.979
11:83265906:A:G	L223P	0.978
11:83274716:C:G	A117P	0.978
11:83280178:A:C	F61L	0.978
11:83280178:A:T	F61L	0.978
11:83280180:A:G	F61L	0.978
11:83274664:A:C	F134C	0.977
11:83265870:A:G	L235P	0.976
11:83274721:A:G	L115P	0.976
11:83261942:A:C	I245R	0.975
11:83261939:G:T	A246E	0.974
11:83274662:C:G	A135P	0.972

dbSNP variants (sampled 300 via entrez): RS1000036127 (11:83267472 C>G,T), RS1000118027 (11:83272858 T>C), RS1000144707 (11:83273451 G>A), RS1000229576 (11:83273361 G>C), RS1000392429 (11:83266996 C>T), RS1000410319 (11:83267299 G>A), RS1000465380 (11:83280622 G>A), RS1000595982 (11:83286288 G>A), RS1000773248 (11:83263277 A>C), RS1000844136 (11:83280368 C>A), RS1000897487 (11:83286484 T>C), RS1001014047 (11:83268223 CATA>C), RS1001201333 (11:83261130 C>G,T), RS1001268331 (11:83272926 C>T), RS1001447741 (11:83272693 A>T)

Disease associations

OMIM: gene MIM:620753 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST010002_244	Refractive error	2.000000e-53
GCST010135_38	Oily fish consumption	9.000000e-09
GCST010140_28	Pork consumption	9.000000e-09
GCST010703_247	Brain morphology (MOSTest)	2.000000e-14

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, decreases methylation	4
Aflatoxin B1	affects expression, decreases methylation, increases expression	4
sodium arsenite	decreases expression, increases expression	3
Particulate Matter	decreases reaction, increases expression, decreases expression, increases abundance	2
dicrotophos	decreases expression	1
chloroacetaldehyde	affects expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
bisphenol S	affects expression	1
MT19c compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Cidofovir	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Vehicle Emissions	decreases reaction, increases expression	1
Cisplatin	decreases expression	1
Demecolcine	increases expression	1
Clodronic Acid	decreases expression	1
Doxorubicin	affects expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Ifosfamide	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Oxygen	affects expression	1
Plant Extracts	increases expression, affects cotreatment	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

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