ATAD3C

Summary

ATAD3C (ATPase family AAA domain containing 3C, HGNC:32151) is a protein-coding gene on chromosome 1p36.33, encoding ATPase family AAA domain-containing protein 3C (Q5T2N8).

Predicted to enable ATP binding activity and ATP hydrolysis activity. Predicted to be involved in mitochondrion organization. Located in mitochondrion.

Source: NCBI Gene 219293 — RefSeq curated summary.

At a glance

• Gene–disease (curated): pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal (Limited, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 143 total — 1 pathogenic
• MANE Select transcript: NM_001039211

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32151
Approved symbol	ATAD3C
Name	ATPase family AAA domain containing 3C
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ34599
Ensembl gene	ENSG00000215915
Ensembl biotype	protein_coding
OMIM	617227
Entrez	219293

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000378785, ENST00000475091, ENST00000484537

RefSeq mRNA: 1 — MANE Select: NM_001039211 NM_001039211

CCDS: CCDS44039

Canonical transcript exons

ENST00000378785 — 12 exons

Exon	Start	End
ENSE00001478728	1468384	1470163
ENSE00001645375	1459161	1459231
ENSE00001654495	1455460	1455519
ENSE00001678337	1452365	1452434
ENSE00001705599	1455791	1455916
ENSE00001711558	1456225	1456349
ENSE00001735727	1462600	1462708
ENSE00001738634	1452046	1452122
ENSE00001780250	1457129	1457180
ENSE00001789344	1454345	1454500
ENSE00001802162	1460750	1460917
ENSE00002305764	1449689	1450758

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 79.41.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2216 / max 18.4644, expressed in 109 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114	0.2216	109

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	79.41	gold quality
right lobe of thyroid gland	UBERON:0001119	78.53	gold quality
adult mammalian kidney	UBERON:0000082	78.28	gold quality
thyroid gland	UBERON:0002046	77.59	gold quality
left lobe of thyroid gland	UBERON:0001120	77.50	gold quality
pancreas	UBERON:0001264	77.42	gold quality
metanephros cortex	UBERON:0010533	76.35	gold quality
cortex of kidney	UBERON:0001225	75.09	gold quality
right lobe of liver	UBERON:0001114	75.06	gold quality
prostate gland	UBERON:0002367	74.65	gold quality
kidney	UBERON:0002113	73.88	gold quality
tibial nerve	UBERON:0001323	73.74	gold quality
urinary bladder	UBERON:0001255	73.71	gold quality
islet of Langerhans	UBERON:0000006	73.13	gold quality
pituitary gland	UBERON:0000007	73.09	gold quality
upper lobe of left lung	UBERON:0008952	73.07	gold quality
gall bladder	UBERON:0002110	72.77	gold quality
sural nerve	UBERON:0015488	72.63	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.08	gold quality
Ammon’s horn	UBERON:0001954	71.43	gold quality
liver	UBERON:0002107	71.15	gold quality
putamen	UBERON:0001874	70.96	gold quality
left uterine tube	UBERON:0001303	70.89	gold quality
adenohypophysis	UBERON:0002196	70.82	gold quality
temporal lobe	UBERON:0001871	70.64	gold quality
amygdala	UBERON:0001876	70.58	gold quality
fallopian tube	UBERON:0003889	70.56	gold quality
bone marrow cell	CL:0002092	70.05	gold quality
saliva-secreting gland	UBERON:0001044	69.82	gold quality
myometrium	UBERON:0001296	69.81	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.56
E-GEOD-110499	no	94.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting ATAD3C, 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-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-6513-5P	99.43	67.81	1071
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-487A-5P	98.85	69.37	993

Literature-anchored findings (GeneRIF, showing 3)

• ATAD3 may therefore be implicated in an unknown but essential and growth-linked mitochondrial function existing since pluri-cellular -organization and involved in tumorigenesis. (PMID:22192748)
• ATAD3C region deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism. (PMID:28549128)
• “ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane”. (PMID:38092275)

Cross-species orthologs

0 orthologs

Paralogs (2): ATAD3B (ENSG00000160072), ATAD3A (ENSG00000197785)

Protein

Protein identifiers

ATPase family AAA domain-containing protein 3C — Q5T2N8 (reviewed: Q5T2N8)

All UniProt accessions (2): Q5T2N8, J3QSF3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the AAA ATPase family.

RefSeq proteins (1): NP_001034300* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003593	AAA+_ATPase	Domain
IPR003959	ATPase_AAA_core	Domain
IPR021911	ATAD3_N	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily

Pfam: PF00004, PF12037

UniProt features (2 total): chain 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T2N8-F1	83.72	0.45

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (1): 177–184

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): TGGNNNNNNKCCAR_UNKNOWN, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, GOMF_ATP_HYDROLYSIS_ACTIVITY, GOMF_ADENYL_NUCLEOTIDE_BINDING, chr1p36, NFKBIA_TARGET_GENES, ZNF596_TARGET_GENES, GOBP_MITOCHONDRION_ORGANIZATION, MIR6756_5P, MIR4723_5P, MIR6870_5P, MIR6766_5P, MIR7111_5P, MIR5698, MIR3175

GO Biological Process (1): mitochondrion organization (GO:0007005)

GO Molecular Function (3): ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), nucleotide binding (GO:0000166)

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle organization	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
ATP-dependent activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

686 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATAD3C	ZNF714	Q96N38	615
ATAD3C	GOLGA6L9	A6NEM1	447
ATAD3C	ADAM18	Q9Y3Q7	443
ATAD3C	ANAPC16	Q96DE5	406
ATAD3C	G3V325	G3V325	374
ATAD3C	C5orf24	Q7Z6I8	369
ATAD3C	CXorf58	Q96LI9	355
ATAD3C	ZNF430	Q9H8G1	353
ATAD3C	CYB5D2	Q8WUJ1	353
ATAD3C	ANKRD13C	Q8N6S4	348
ATAD3C	DCAF10	Q5QP82	347
ATAD3C	MYO5C	Q9NQX4	339
ATAD3C	C2orf69	Q8N8R5	336
ATAD3C	ARL11	Q969Q4	330
ATAD3C	MRTFA	Q969V6	328

IntAct

20 interactions, top by confidence:

A	B	Type	Score
COMMD1	VPS26C	psi-mi:“MI:0914”(association)	0.730
ESR1	TRIM24	psi-mi:“MI:0914”(association)	0.640
DKK3	NME4	psi-mi:“MI:0914”(association)	0.530
BRD1	KAT7	psi-mi:“MI:0914”(association)	0.530
GDE1	GAPDHS	psi-mi:“MI:0914”(association)	0.530
HSPA8	PPP6C	psi-mi:“MI:0914”(association)	0.350
DLST		psi-mi:“MI:0914”(association)	0.350
METTL14	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
ABHD11	NME4	psi-mi:“MI:0914”(association)	0.350
DKK3	MYO9A	psi-mi:“MI:0914”(association)	0.350
PLEKHM3	ENDOD1	psi-mi:“MI:0914”(association)	0.350
PLCD4	MLLT3	psi-mi:“MI:0914”(association)	0.350
RDH13	SELENBP1	psi-mi:“MI:0914”(association)	0.350
PTH1R	ATAD3C	psi-mi:“MI:0914”(association)	0.350
PHKG2	NDUFA4	psi-mi:“MI:0914”(association)	0.350
	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (45): ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-RNA), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Synthetic Lethality), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS), ATAD3C (Affinity Capture-MS)

ESM2 similar proteins: A2C563, A3KMH1, A4FUD9, B0R0T1, B7K9M6, O14134, O48534, O60072, O94248, P0DUG1, P18708, P18759, P24487, P29458, P29551, P34732, P41389, P46459, P46460, P46461, P49739, P54351, Q09580, Q0E3C8, Q0WVF5, Q12019, Q1DKI1, Q26454, Q28BS0, Q3MEF4, Q46IJ6, Q5NBJ3, Q5R410, Q5T2N8, Q5YLB4, Q6DW73, Q75JI3, Q7ZXZ0, Q8CC88, Q8T5T1

Diamond homologs: A7YWC4, C8W731, D1C4U5, D5H7Z5, O27092, P42811, Q20748, Q3KRE0, Q58889, Q58E76, Q5T2N8, Q5T9A4, Q6NVR9, Q6PAX2, Q925I1, Q9NVI7, Q9VEX6, A7I8B8, B3DV46, C7N914, D7Y2H4, O26824, O64982, P03974, P0DKJ9, P0DKK0, P23787, P25694, P32795, P46462, P54811, P54812, P55072, P73437, Q01853, Q01939, Q05AS3, Q2NIN5, Q3ULF4, Q3UMC0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	112
Likely benign	12
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
225699	Single allele	Pathogenic

SpliceAI

2506 predictions. Top by Δscore:

Variant	Effect	Δscore
1:1450670:T:TA	acceptor_gain	1.0000
1:1450673:A:AG	acceptor_gain	1.0000
1:1450673:ATCT:A	acceptor_gain	1.0000
1:1450674:T:G	acceptor_gain	1.0000
1:1450676:TGCA:T	acceptor_loss	1.0000
1:1450677:GCAG:G	acceptor_loss	1.0000
1:1450678:CAGGC:C	acceptor_loss	1.0000
1:1450679:A:AG	acceptor_gain	1.0000
1:1450679:A:T	acceptor_loss	1.0000
1:1450679:AG:A	acceptor_gain	1.0000
1:1450680:G:A	acceptor_loss	1.0000
1:1450680:G:GT	acceptor_gain	1.0000
1:1450680:GG:G	acceptor_gain	1.0000
1:1450680:GGC:G	acceptor_gain	1.0000
1:1450680:GGCC:G	acceptor_gain	1.0000
1:1450680:GGCCA:G	acceptor_gain	1.0000
1:1450754:TCAAA:T	donor_gain	1.0000
1:1450755:CAAA:C	donor_gain	1.0000
1:1450756:AAA:A	donor_gain	1.0000
1:1450757:AA:A	donor_gain	1.0000
1:1450758:AG:A	donor_loss	1.0000
1:1450759:GTG:G	donor_loss	1.0000
1:1450759:GTGA:G	donor_gain	1.0000
1:1452030:T:TA	acceptor_gain	1.0000
1:1452032:C:CA	acceptor_gain	1.0000
1:1452033:G:A	acceptor_gain	1.0000
1:1452042:TCAGC:T	acceptor_loss	1.0000
1:1452044:A:AG	acceptor_gain	1.0000
1:1452045:G:GA	acceptor_gain	1.0000
1:1452045:GC:G	acceptor_gain	1.0000

AlphaMissense

2671 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:1457160:T:C	F241L	0.907
1:1457162:C:A	F241L	0.907
1:1457162:C:G	F241L	0.907
1:1456321:T:C	F221L	0.872
1:1456323:T:A	F221L	0.872
1:1456323:T:G	F221L	0.872
1:1460769:A:C	S278R	0.865
1:1460771:C:A	S278R	0.865
1:1460771:C:G	S278R	0.865
1:1456329:G:C	W223C	0.860
1:1456329:G:T	W223C	0.860
1:1454367:C:A	A82D	0.845
1:1460751:T:C	F272L	0.843
1:1460753:C:A	F272L	0.843
1:1460753:C:G	F272L	0.843
1:1456327:T:A	W223R	0.830
1:1456327:T:C	W223R	0.830
1:1459200:T:C	F261L	0.828
1:1459202:C:A	F261L	0.828
1:1459202:C:G	F261L	0.828
1:1460829:T:C	F298L	0.824
1:1460831:C:A	F298L	0.824
1:1460831:C:G	F298L	0.824
1:1462619:T:C	F334L	0.819
1:1462621:T:A	F334L	0.819
1:1462621:T:G	F334L	0.819
1:1462703:T:A	W362R	0.819
1:1462703:T:C	W362R	0.819
1:1454385:C:A	A88D	0.805
1:1456232:C:A	A191D	0.799

dbSNP variants (sampled 300 via entrez): RS1000047313 (1:1450019 G>A), RS1000156470 (1:1452581 G>A), RS1000252541 (1:1462147 C>A), RS1000444576 (1:1452978 G>A), RS1000446269 (1:1450618 GC>G), RS1000503434 (1:1455503 A>G), RS1000577711 (1:1466103 G>A,T), RS1000588451 (1:1461194 T>C), RS1000642729 (1:1467225 C>T), RS1000812964 (1:1457512 C>G,T), RS1001060216 (1:1470109 T>G), RS1001164978 (1:1458966 C>A,T), RS1001252772 (1:1461566 G>A), RS1001429441 (1:1469294 A>G), RS1001468770 (1:1464437 G>A,C)

Disease associations

OMIM: gene MIM:617227 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal	Limited	Unknown

Mondo (1): pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal (MONDO:0032931)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005951_34	Body mass index	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	increases abundance, increases expression, decreases expression	2
sotorasib	affects cotreatment, decreases expression	1
propionaldehyde	decreases expression	1
bisphenol A	decreases expression	1
beta-lapachone	decreases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
benzo(e)pyrene	increases methylation	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Cadmium	increases abundance, increases palmitoylation, decreases reaction	1
Estradiol	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Smoke	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	increases palmitoylation, decreases reaction, increases abundance	1
Okadaic Acid	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_C6PY	ESi118-A	Induced pluripotent stem cell	Male

Clinical trials (associated diseases)

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