RTL10

Summary

RTL10 (retrotransposon Gag like 10, HGNC:26112) is a protein-coding gene on chromosome 22q11.21, encoding Protein Bop (Q7L3V2). Could induce apoptosis in a BH3 domain-dependent manner.

Involved in mitochondrial outer membrane permeabilization and regulation of mitochondrial membrane potential. Located in mitochondrion.

Source: NCBI Gene 79680 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_024627

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26112
Approved symbol	RTL10
Name	retrotransposon Gag like 10
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21125, BOP
Ensembl gene	ENSG00000215012
Ensembl biotype	protein_coding
OMIM	620751
Entrez	79680

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000328554, ENST00000405640, ENST00000407472, ENST00000416337, ENST00000484072

RefSeq mRNA: 1 — MANE Select: NM_024627 NM_024627

CCDS: CCDS13769

Canonical transcript exons

ENST00000328554 — 3 exons

Exon	Start	End
ENSE00001364867	19854660	19854874
ENSE00001558592	19846146	19852486
ENSE00003489628	19854443	19854539

Expression profiles

Bgee: expression breadth ubiquitous, 223 present calls, max score 94.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.8977 / max 216.6662, expressed in 1735 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193167	11.8977	1735
193166	11.0144	1741

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	94.98	gold quality
endothelial cell	CL:0000115	93.48	silver quality
stromal cell of endometrium	CL:0002255	86.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.60	gold quality
middle temporal gyrus	UBERON:0002771	85.17	silver quality
lower esophagus mucosa	UBERON:0035834	84.93	gold quality
hair follicle	UBERON:0002073	84.84	gold quality
Brodmann (1909) area 23	UBERON:0013554	83.81	gold quality
right frontal lobe	UBERON:0002810	83.41	gold quality
cerebellar vermis	UBERON:0004720	82.44	silver quality
right hemisphere of cerebellum	UBERON:0014890	81.94	gold quality
primary visual cortex	UBERON:0002436	81.71	gold quality
cerebellar hemisphere	UBERON:0002245	81.49	gold quality
cerebellar cortex	UBERON:0002129	81.45	gold quality
germinal epithelium of ovary	UBERON:0001304	81.41	silver quality
anterior cingulate cortex	UBERON:0009835	80.88	gold quality
cingulate cortex	UBERON:0003027	80.77	gold quality
cerebellum	UBERON:0002037	80.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.62	gold quality
neocortex	UBERON:0001950	80.58	gold quality
frontal cortex	UBERON:0001870	80.54	gold quality
upper leg skin	UBERON:0004262	80.45	gold quality
ventricular zone	UBERON:0003053	80.32	gold quality
prefrontal cortex	UBERON:0000451	80.28	gold quality
skin of leg	UBERON:0001511	79.91	gold quality
duodenum	UBERON:0002114	79.57	gold quality
tongue squamous epithelium	UBERON:0006919	79.55	silver quality
cortical plate	UBERON:0005343	79.36	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	79.28	gold quality
cerebral cortex	UBERON:0000956	79.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.75
E-CURD-11	no	182.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting RTL10, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-1184	99.99	68.19	1458
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-302E	99.96	70.74	2669
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-609	99.82	64.26	505
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-1197	99.70	67.75	1027
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-1260A	99.61	66.67	1098

Literature-anchored findings (GeneRIF, showing 5)

• Bop may be a novel BH3-only factor that can engage with the regulatory network of Bcl-2 family members to process intrinsic apoptotic signaling (PMID:23055042)
• Members of the subfamily of BH3-only proteins function as proapoptotic triggers, and mimetics of these proteins are already in clinical trials in other cancers. (PMID:24673301)
• Studies indicate that BH3-only protein (C22orf29 protein) plays an important role in activation and communication in apoptosis pathways. (PMID:25404273)
• The BH3-only proteins were required for apoptosis induced as a result of BCL-XL inhibition, this requirement was overcome when both BCL-XL and MCL-1 were inhibited, implicating distinct mechanisms by which different anti-apoptotic BCL-2 family members may regulate apoptosis in cancer. (PMID:30185825)
• BH3-only protein expression determines hepatocellular carcinoma response to sorafenib-based treatment. (PMID:34312366)

Cross-species orthologs

0 orthologs

Paralogs (10): RTL8C (ENSG00000134590), RTL3 (ENSG00000179300), LDOC1 (ENSG00000182195), RTL4 (ENSG00000187823), RTL6 (ENSG00000188636), RTL8A (ENSG00000203950), RTL8B (ENSG00000212747), PEG10 (ENSG00000242265), RTL5 (ENSG00000242732), RTL1 (ENSG00000254656)

Protein

Protein identifiers

Protein Bop — Q7L3V2 (reviewed: Q7L3V2)

Alternative names: BH3-only protein, Retrotransposon Gag-like protein 10

All UniProt accessions (2): C9J0V4, Q7L3V2

UniProt curated annotations — full annotation on UniProt →

Function. Could induce apoptosis in a BH3 domain-dependent manner. The direct interaction network of Bcl-2 family members may play a key role in modulation RTL10/BOP intrinsic apoptotic signaling activity.

Subunit / interactions. Interacts (via BH3 domain) with VDAC1. Interacts with pro-survival Bcl-2 family members, BCL2, BCL2L1 isoform Bcl-X(L), MCL1, BCL2A1 and BCL2L2. Interacts with BAX and BAK1.

Subcellular location. Mitochondrion.

Tissue specificity. Ubiquitously expressed.

Domain organisation. The BH3 motif is required for pro-apoptotic activity and for interaction with pro-survival Bcl-2 family members.

RefSeq proteins (1): NP_078903* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032549	RTL1/1-8/LDOC_capsid-like	Domain

Pfam: PF16297

UniProt features (14 total): mutagenesis site 4, region of interest 2, sequence conflict 2, compositionally biased region 2, sequence variant 2, chain 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L3V2-F1	54.98	0.12

Functional residue map

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

Mutagenesis-validated functional residues (4):

Position	Phenotype
122	no effect on interaction with vdac1.
123	reduces the pro-apoptotic activity, no effect on interaction with vdac1.
118	reduces the pro-apoptotic activity and interaction with vdac1.
120	no effect on interaction with vdac1.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 69 (showing top): GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_MITOCHONDRIAL_TRANSPORT, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GRE_C, GATA1_03, GOBP_REGULATION_OF_MITOCHONDRIAL_MEMBRANE_POTENTIAL, TGGNNNNNNKCCAR_UNKNOWN, RYTTCCTG_ETS2_B, GOBP_MEMBRANE_ORGANIZATION, GOBP_REGULATION_OF_MEMBRANE_PERMEABILITY, AR_01, TGGAAA_NFAT_Q4_01, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, GOBP_REGULATION_OF_MEMBRANE_POTENTIAL

GO Biological Process (3): regulation of mitochondrial membrane potential (GO:0051881), mitochondrial outer membrane permeabilization (GO:0097345), apoptotic process (GO:0006915)

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
apoptotic signaling pathway	2
regulation of membrane potential	1
positive regulation of mitochondrial membrane permeability involved in apoptotic process	1
programmed cell death	1
execution phase of apoptosis	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

628 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RTL10	BCL2	P10415	989
RTL10	BCL2L1	Q07817	972
RTL10	MCL1	Q07820	942
RTL10	BCL2L11	O43521	877
RTL10	PMAIP1	Q13794	840
RTL10	BCL2L2-PABPN1	Q92843	822
RTL10	CYCS	P00001	720
RTL10	BECN1	Q14457	719
RTL10	BMF	Q96LC9	716
RTL10	HRK	O00198	696
RTL10	BCL2A1	Q16548	679
RTL10	BIK	Q13323	669
RTL10	CASP8	Q14790	669
RTL10	BBC3	Q96PG8	660
RTL10	BNIP3	Q12983	644

IntAct

27 interactions, top by confidence:

A	B	Type	Score
BCL2L1	BAK1	psi-mi:“MI:0914”(association)	0.940
RTL10	GPRASP2	psi-mi:“MI:0915”(physical association)	0.620
GPRASP2	RTL10	psi-mi:“MI:0915”(physical association)	0.620
BCL2L2	RTL10	psi-mi:“MI:0915”(physical association)	0.580
RTL10	BCL2L2	psi-mi:“MI:0915”(physical association)	0.580
RTL10	BCL2L2	psi-mi:“MI:0914”(association)	0.580
VDAC1	RTL10	psi-mi:“MI:0915”(physical association)	0.540
VDAC1	RTL10	psi-mi:“MI:0407”(direct interaction)	0.540
RTL10	MCL1	psi-mi:“MI:0915”(physical association)	0.500
RTL10	BCL2L1	psi-mi:“MI:0914”(association)	0.460
RTL10	BAK1	psi-mi:“MI:0915”(physical association)	0.400
RTL10	BAX	psi-mi:“MI:0915”(physical association)	0.400
BCL2A1	RTL10	psi-mi:“MI:0915”(physical association)	0.400
RTL10	PLCG2	psi-mi:“MI:0915”(physical association)	0.370
RTL10	BCL2	psi-mi:“MI:0914”(association)	0.350
BCL2	RTL10	psi-mi:“MI:0914”(association)	0.350
RTL10	INPPL1	psi-mi:“MI:0914”(association)	0.350
GPRASP2	GYG2	psi-mi:“MI:0914”(association)	0.350
CDKN3	CST8	psi-mi:“MI:0914”(association)	0.350
FDFT1	CDC45	psi-mi:“MI:0914”(association)	0.350
DSCAM	RTL10	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): BRCA1 (Two-hybrid), C22orf29 (Two-hybrid), C22orf29 (Affinity Capture-RNA), GPRASP2 (Two-hybrid), C22orf29 (Affinity Capture-RNA), C22orf29 (Affinity Capture-MS), C22orf29 (Affinity Capture-MS), C22orf29 (Affinity Capture-MS), ARNT (Affinity Capture-MS), INPPL1 (Affinity Capture-MS), TGFBRAP1 (Affinity Capture-MS), VPS11 (Affinity Capture-MS), RIPK1 (Affinity Capture-MS), C22orf29 (Two-hybrid)

ESM2 similar proteins: A1YEW3, A1YG31, A2T715, A2T7M0, A6NEV1, A6NGD5, A6NJL1, A6QPT6, A8MXV6, A8MZF0, A8WFF7, O08664, P03327, P06936, P0C6A0, P0DPQ3, P54257, P57086, P86478, P86479, P86480, P86481, P86496, Q13487, Q32PG5, Q505G4, Q5R7P6, Q68FX5, Q6J1H4, Q6NZN1, Q6ZMS7, Q6ZRT6, Q76NI1, Q7L3V2, Q7TPK6, Q7YR42, Q7Z6I6, Q80UE6, Q8IY33, Q8K2W9

Diamond homologs: A6ZKI3, O95751, Q17QF6, Q17RB0, Q1JQ94, Q505G4, Q5DTT4, Q5HYW3, Q5R6M8, Q6ICC9, Q6SEH4, Q6SEH5, Q7L3V2, Q7TPY9, Q9BWD3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 17 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.

GO biological processes:

GO term	Partners	Fold	FDR
release of cytochrome c from mitochondria	7	307.2×	2e-14
extrinsic apoptotic signaling pathway in absence of ligand	7	204.8×	2e-13
intrinsic apoptotic signaling pathway in response to DNA damage	7	141.8×	2e-12
positive regulation of apoptotic process	8	28.4×	8e-09
negative regulation of apoptotic process	6	13.0×	6e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

528 predictions. Top by Δscore:

Variant	Effect	Δscore
22:19851732:T:TA	donor_gain	0.9900
22:19854439:CCA:C	donor_loss	0.9900
22:19854440:CA:C	donor_loss	0.9900
22:19854441:A:C	donor_loss	0.9900
22:19854442:C:CT	donor_loss	0.9900
22:19854818:AC:A	donor_gain	0.9900
22:19854819:CC:C	donor_gain	0.9900
22:19854819:CCCT:C	donor_gain	0.9900
22:19851705:G:C	donor_gain	0.9800
22:19854439:CCACC:C	donor_gain	0.9800
22:19854826:G:A	donor_gain	0.9800
22:19854670:AGG:A	donor_gain	0.9700
22:19854694:G:GT	donor_gain	0.9700
22:19854816:TGA:T	donor_loss	0.9600
22:19854817:GA:G	donor_loss	0.9600
22:19854819:C:CA	donor_loss	0.9600
22:19847390:CTG:C	acceptor_gain	0.9500
22:19854670:AGGC:A	donor_gain	0.9500
22:19854691:TGC:T	donor_gain	0.9500
22:19854692:GCG:G	donor_gain	0.9500
22:19854814:ACTG:A	donor_loss	0.9500
22:19854812:ACAC:A	donor_loss	0.9400
22:19854813:CACT:C	donor_loss	0.9400
22:19854818:A:AC	donor_gain	0.9400
22:19854819:C:CC	donor_gain	0.9400
22:19854815:C:CA	donor_loss	0.9300
22:19854816:T:TG	donor_loss	0.9300
22:19854817:G:GG	donor_loss	0.9300
22:19854819:C:T	donor_loss	0.9300
22:19851704:A:AC	donor_gain	0.9200

AlphaMissense

2344 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:19851911:G:C	F117L	0.952
22:19851911:G:T	F117L	0.952
22:19851913:A:G	F117L	0.952
22:19851749:G:C	F171L	0.942
22:19851749:G:T	F171L	0.942
22:19851751:A:G	F171L	0.942
22:19851881:G:C	F127L	0.938
22:19851881:G:T	F127L	0.938
22:19851883:A:G	F127L	0.938
22:19851941:A:C	F107L	0.926
22:19851941:A:T	F107L	0.926
22:19851943:A:G	F107L	0.926
22:19851605:G:C	F219L	0.907
22:19851605:G:T	F219L	0.907
22:19851607:A:G	F219L	0.907
22:19851974:G:C	F96L	0.882
22:19851974:G:T	F96L	0.882
22:19851976:A:G	F96L	0.882
22:19851912:A:G	F117S	0.881
22:19851750:A:C	F171C	0.854
22:19852126:A:G	W46R	0.846
22:19852126:A:T	W46R	0.846
22:19851803:C:A	W153C	0.844
22:19851803:C:G	W153C	0.844
22:19851875:A:C	F129L	0.830
22:19851875:A:T	F129L	0.830
22:19851877:A:G	F129L	0.830
22:19851805:A:G	W153R	0.823
22:19851805:A:T	W153R	0.823
22:19851912:A:C	F117C	0.817

dbSNP variants (sampled 300 via entrez): RS1000368319 (22:19855966 T>C), RS1000384144 (22:19850952 A>G), RS1000392784 (22:19848489 G>A,T), RS1000420615 (22:19855741 A>C,G), RS1000758585 (22:19847502 G>A), RS1000835198 (22:19847276 C>G), RS1000989566 (22:19853130 C>T), RS1001042147 (22:19847053 C>T), RS1001156203 (22:19847278 G>A), RS1001336689 (22:19852872 T>C,G), RS1001621703 (22:19846134 A>C), RS1001862618 (22:19853191 A>G), RS1002046543 (22:19848061 C>T), RS1002158667 (22:19848272 C>T), RS1002484633 (22:19846341 C>A,T)

Disease associations

OMIM: gene MIM:620751 | 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

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Formaldehyde	decreases expression	2
dicrotophos	increases expression	1
bisphenol A	increases expression	1
o,p’-DDT	increases expression	1
sulforaphane	decreases expression	1
sodium arsenite	decreases expression	1
diallyl trisulfide	increases expression	1
abrine	decreases expression	1
Resveratrol	increases expression	1
Arsenicals	decreases expression	1
Calcitriol	increases expression	1
Doxorubicin	decreases expression	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
Zearalenone	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Genistein	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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