C10orf88

Summary

C10orf88 (chromosome 10 open reading frame 88, HGNC:25822) is a protein-coding gene on chromosome 10q26.13, encoding ATPase PAAT (Q9H8K7). ATPase that regulates mitochondrial ABC transporters ABCB7, ABCB8/MITOSUR and ABCB10.

Enables ATP hydrolysis activity. Located in mitochondrion.

Source: NCBI Gene 80007 — RefSeq curated summary.

At a glance

• GWAS associations: 16
• Clinical variants (ClinVar): 13 total — 1 pathogenic
• MANE Select transcript: NM_024942

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25822
Approved symbol	C10orf88
Name	chromosome 10 open reading frame 88
Location	10q26.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13490, Em:AC073585.5, PAAT
Ensembl gene	ENSG00000119965
Ensembl biotype	protein_coding
OMIM	620661
Entrez	80007

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000368891, ENST00000462191, ENST00000470158, ENST00000481909

RefSeq mRNA: 1 — MANE Select: NM_024942 NM_024942

CCDS: CCDS7632

Canonical transcript exons

ENST00000481909 — 6 exons

Exon	Start	End
ENSE00000933515	122952829	122953032
ENSE00001795186	122954015	122954227
ENSE00001851945	122930901	122932661
ENSE00003584458	122951954	122952026
ENSE00003681947	122937705	122938159
ENSE00003693528	122948649	122948855

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 87.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.8577 / max 91.6704, expressed in 1698 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
111771	5.7185	1693
111772	0.1392	30

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.91	gold quality
cortical plate	UBERON:0005343	87.80	gold quality
right testis	UBERON:0004534	85.75	gold quality
left testis	UBERON:0004533	85.47	gold quality
testis	UBERON:0000473	85.03	gold quality
ganglionic eminence	UBERON:0004023	84.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.21	gold quality
ventricular zone	UBERON:0003053	81.40	gold quality
prefrontal cortex	UBERON:0000451	81.39	gold quality
adrenal tissue	UBERON:0018303	80.04	gold quality
islet of Langerhans	UBERON:0000006	79.79	gold quality
calcaneal tendon	UBERON:0003701	79.59	gold quality
stromal cell of endometrium	CL:0002255	79.37	gold quality
sperm	CL:0000019	78.87	gold quality
hindlimb stylopod muscle	UBERON:0004252	78.83	gold quality
cerebellar hemisphere	UBERON:0002245	78.53	gold quality
cerebellar cortex	UBERON:0002129	78.47	gold quality
gastrocnemius	UBERON:0001388	78.46	gold quality
rectum	UBERON:0001052	78.45	gold quality
muscle of leg	UBERON:0001383	78.45	gold quality
Brodmann (1909) area 9	UBERON:0013540	78.08	gold quality
granulocyte	CL:0000094	77.89	gold quality
right hemisphere of cerebellum	UBERON:0014890	77.74	gold quality
right adrenal gland	UBERON:0001233	77.70	gold quality
right adrenal gland cortex	UBERON:0035827	77.67	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	77.56	gold quality
secondary oocyte	CL:0000655	77.33	gold quality
ovary	UBERON:0000992	77.30	gold quality
monocyte	CL:0000576	77.29	gold quality
leukocyte	CL:0000738	77.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

88 targeting C10orf88, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-551B-5P	99.96	71.28	3493
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-101-3P	99.94	75.03	2230
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-153-5P	99.89	73.86	6317
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-576-5P	99.84	70.46	2582

Literature-anchored findings (GeneRIF, showing 2)

• Regulates iron transport into the mitochondria (PMID:25063848)
• Our results suggest that rare protein-altering variants in the C10orf88 and UNC93B1 genes are associated with a worse response to anti-VEGF therapy in patients with neovascular age-related macular degeneration, but these results require further validation in other cohorts. (PMID:29852030)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:rp71-19m20.1	ENSDARG00000089828
mus_musculus	2310057M21Rik	ENSMUSG00000040177
rattus_norvegicus	C1h10orf88	ENSRNOG00000020597

Protein

Protein identifiers

ATPase PAAT — Q9H8K7 (reviewed: Q9H8K7)

Alternative names: Protein associated with ABC transporters

All UniProt accessions (1): Q9H8K7

UniProt curated annotations — full annotation on UniProt →

Function. ATPase that regulates mitochondrial ABC transporters ABCB7, ABCB8/MITOSUR and ABCB10. Regulates mitochondrial ferric concentration and heme biosynthesis and plays a role in the maintenance of mitochondrial homeostasis and cell survival.

Subunit / interactions. Homodimer. Interacts with ABCB7, ABCB8/MITOSUR and ABCB10.

Subcellular location. Cytoplasm. Mitochondrion.

RefSeq proteins (1): NP_079218* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028043	PAAT-like	Family

Pfam: PF14958

Catalyzed reactions (Rhea), 1 shown:

• ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)

UniProt features (8 total): modified residue 4, 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-Q9H8K7-F1	66.48	0.24

Functional residue map

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

Post-translational modifications (4): 177, 182, 254, 302

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOMF_ATP_HYDROLYSIS_ACTIVITY, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_UP, BRUINS_UVC_RESPONSE_MIDDLE, BAKKER_FOXO3_TARGETS_DN, LEE_BMP2_TARGETS_DN, ALKBH3_TARGET_GENES, GSE10240_IL22_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, CEBPZ_TARGET_GENES, DACH1_TARGET_GENES, GLI4_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (4): ATP hydrolysis activity (GO:0016887), identical protein binding (GO:0042802), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (2): cytoplasm (GO:0005737), mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribonucleoside triphosphate phosphatase activity	1
ATP-dependent activity	1
protein binding	1
binding	1
catalytic activity	1
intracellular anatomical structure	1
cellular anatomical structure	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

740 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C10orf88	NADSYN1	Q6IA69	655
C10orf88	CYP2R1	Q6VVX0	570
C10orf88	TEX9	Q8N6V9	556
C10orf88	C19orf44	Q9H6X5	543
C10orf88	CCDC91	Q7Z6B0	527
C10orf88	UTP3	Q9NQZ2	495
C10orf88	NCKAP1	Q9Y2A7	467
C10orf88	GDI2	P50395	464
C10orf88	DHCR7	Q9UBM7	447
C10orf88	CLTC	Q00610	433
C10orf88	PROSER3	Q2NL68	430
C10orf88	CLTCL1	P53675	430
C10orf88	LILRB4	Q8NHJ6	429
C10orf88	CYP24A1	Q07973	419
C10orf88	ACADSB	P45954	418

IntAct

78 interactions, top by confidence:

A	B	Type	Score
MAP2K5	MAPK7	psi-mi:“MI:0914”(association)	0.860
PHC1	CBX4	psi-mi:“MI:0914”(association)	0.790
PAAT	CLTC	psi-mi:“MI:0914”(association)	0.740
LNX1	PAAT	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	PAAT	psi-mi:“MI:0915”(physical association)	0.560
PKNOX2	PAAT	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	PAAT	psi-mi:“MI:0915”(physical association)	0.560
CASP6	PAAT	psi-mi:“MI:0915”(physical association)	0.560
CHAT	PAAT	psi-mi:“MI:0915”(physical association)	0.560
PAAT	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
PAAT	GSN	psi-mi:“MI:0915”(physical association)	0.560
RAN	PAAT	psi-mi:“MI:0915”(physical association)	0.560
PAAT	LNX2	psi-mi:“MI:0915”(physical association)	0.550
LNX2	PAAT	psi-mi:“MI:0915”(physical association)	0.550
GDI2	FN1	psi-mi:“MI:0914”(association)	0.530
PAAT	PAAT	psi-mi:“MI:0915”(physical association)	0.370
Nedd1		psi-mi:“MI:0914”(association)	0.350

BioGRID (141): C10orf88 (Two-hybrid), C10orf88 (Proximity Label-MS), C10orf88 (Two-hybrid), C10orf88 (Affinity Capture-MS), C10orf88 (Affinity Capture-MS), C10orf88 (Affinity Capture-MS), DOCK11 (Affinity Capture-MS), DOCK9 (Affinity Capture-MS), NEDD1 (Affinity Capture-MS), C10orf88 (Affinity Capture-MS), C10orf88 (Affinity Capture-MS), NCKAP1 (Affinity Capture-MS), C10orf88 (Affinity Capture-MS), C10orf88 (Affinity Capture-MS), C10orf88 (Affinity Capture-MS)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A4D1B5, A4FUB0, D3IUT5, D3Z6S9, F1QB81, O60281, O70167, P53995, Q0VCQ7, Q13129, Q14699, Q2T9I9, Q3TCV3, Q3UJC8, Q402B2, Q4R9E9, Q5RA75, Q5RB52, Q5XI46, Q5XI56, Q5ZKI7, Q659A1, Q6AYM1, Q6DRL4, Q6INI0, Q6PUR7, Q7Z2Z1, Q8BQ33, Q8CCC3, Q8CDN1, Q8IXR9, Q8K1K4, Q8NB91, Q8ND61, Q90WN7, Q920I9, Q92674

Diamond homologs: Q499Y3, Q5XI46, Q9D2Q3, Q9H8K7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 70 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Clathrin-mediated endocytosis	7	12.7×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	5
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2684621	GRCh37/hg19 10q25.1-26.3(chr10:111447991-133435388)x3	Pathogenic

SpliceAI

1143 predictions. Top by Δscore:

Variant	Effect	Δscore
10:122952024:TCA:T	acceptor_gain	1.0000
10:122952025:CA:C	acceptor_gain	1.0000
10:122952025:CAC:C	acceptor_gain	1.0000
10:122952027:C:CC	acceptor_gain	1.0000
10:122932662:C:CC	acceptor_gain	0.9900
10:122938155:CAATT:C	acceptor_gain	0.9900
10:122948856:C:CC	acceptor_gain	0.9900
10:122951947:AACTT:A	donor_loss	0.9900
10:122951948:ACTTA:A	donor_loss	0.9900
10:122951949:CTT:C	donor_loss	0.9900
10:122951950:TTAC:T	donor_loss	0.9900
10:122951951:TA:T	donor_loss	0.9900
10:122951952:A:AA	donor_loss	0.9900
10:122952022:GTTCA:G	acceptor_gain	0.9900
10:122952023:TTCA:T	acceptor_gain	0.9900
10:122952024:TCAC:T	acceptor_loss	0.9900
10:122952026:ACT:A	acceptor_loss	0.9900
10:122952027:C:T	acceptor_loss	0.9900
10:122952028:T:A	acceptor_loss	0.9900
10:122952898:T:TA	donor_gain	0.9900
10:122953957:C:A	donor_gain	0.9900
10:122954013:AC:A	donor_gain	0.9900
10:122954014:C:CA	donor_gain	0.9900
10:122954117:T:TA	donor_gain	0.9900
10:122954118:C:A	donor_gain	0.9900
10:122954159:T:TA	donor_gain	0.9900
10:122954222:T:TA	donor_gain	0.9900
10:122954276:T:TA	donor_gain	0.9900
10:122932657:CCATT:C	acceptor_gain	0.9800
10:122932658:CATTC:C	acceptor_gain	0.9800

AlphaMissense

2927 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:122952915:A:C	S94R	0.995
10:122952915:A:T	S94R	0.995
10:122952917:T:G	S94R	0.995
10:122948677:A:G	L207S	0.986
10:122948854:A:G	L148S	0.976
10:122952878:A:G	Y107H	0.974
10:122951954:C:A	K147N	0.959
10:122951954:C:G	K147N	0.959
10:122932587:A:G	L393P	0.958
10:122932554:A:G	L404P	0.957
10:122952860:C:G	G113R	0.954
10:122954121:A:G	W20R	0.948
10:122954121:A:T	W20R	0.948
10:122952004:A:C	Y131D	0.946
10:122952877:T:C	Y107C	0.945
10:122952897:T:A	E100D	0.944
10:122952897:T:G	E100D	0.944
10:122952980:A:G	C73R	0.944
10:122952906:T:A	R97S	0.943
10:122952906:T:G	R97S	0.943
10:122952859:C:T	G113D	0.941
10:122952910:G:T	A96E	0.941
10:122951958:A:T	I146K	0.939
10:122952877:T:G	Y107S	0.935
10:122948665:A:T	V211D	0.933
10:122932596:T:A	E390V	0.932
10:122952859:C:A	G113V	0.932
10:122954119:C:A	W20C	0.931
10:122954119:C:G	W20C	0.931
10:122952978:G:C	C73W	0.928

dbSNP variants (sampled 300 via entrez): RS1000088044 (10:122955591 C>A,T), RS1000152254 (10:122946476 G>A), RS1000205165 (10:122946135 A>G), RS1000515615 (10:122932112 C>T), RS1000530828 (10:122947785 T>C), RS1000693920 (10:122954434 G>A), RS1000694628 (10:122939574 T>A), RS1000751488 (10:122953263 G>A,C), RS1001093770 (10:122939279 A>C), RS1001209040 (10:122946891 C>T), RS1001241354 (10:122938441 G>A,T), RS1001309695 (10:122945631 G>A), RS1001441890 (10:122939563 T>C), RS1001773124 (10:122936137 G>A,C), RS1001884075 (10:122930998 G>A)

Disease associations

OMIM: gene MIM:620661 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST006612_7	LDL cholesterol	1.000000e-14
GCST006804_142	Red cell distribution width	4.000000e-10
GCST008077_27	LDL cholesterol levels	4.000000e-06
GCST008077_67	LDL cholesterol levels	3.000000e-09
GCST008078_108	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	4.000000e-13
GCST008078_29	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	8.000000e-10
GCST008079_150	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	2.000000e-15
GCST008079_55	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	3.000000e-11
GCST008086_31	LDL cholesterol levels in current drinkers	2.000000e-06
GCST008086_64	LDL cholesterol levels in current drinkers	1.000000e-09
GCST010243_24	Apolipoprotein B levels	5.000000e-13
GCST010245_106	LDL cholesterol levels	7.000000e-14
GCST90002385_490	High light scatter reticulocyte count	3.000000e-11
GCST90002386_411	High light scatter reticulocyte percentage of red cells	3.000000e-11
GCST90002396_498	Mean reticulocyte volume	9.000000e-13
GCST90002404_500	Red cell distribution width	2.000000e-40

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0009188	Red cell distribution width
EFO:0004329	alcohol drinking
EFO:0004615	apolipoprotein B measurement
EFO:0007986	reticulocyte count
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	3
Valproic Acid	affects expression, decreases expression	3
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
sodium arsenite	increases expression	1
pentabromodiphenyl ether	increases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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