IFFO1

gene
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Also known as HOM-TES-103

Summary

IFFO1 (intermediate filament family orphan 1, HGNC:24970) is a protein-coding gene on chromosome 12p13.31, encoding Non-homologous end joining factor IFFO1 (Q0D2I5). Nuclear matrix protein involved in the immobilization of broken DNA ends and the suppression of chromosome translocation during DNA double-strand breaks (DSBs).

This gene is a member of the intermediate filament family. Intermediate filaments are proteins which are primordial components of the cytoskeleton and nuclear envelope. The proteins encoded by the members of this gene family are evolutionarily and structurally related but have limited sequence homology, with the exception of the central rod domain. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 25900 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 101 total
  • MANE Select transcript: NM_001193457

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24970
Approved symbolIFFO1
Nameintermediate filament family orphan 1
Location12p13.31
Locus typegene with protein product
StatusApproved
AliasesHOM-TES-103
Ensembl geneENSG00000010295
Ensembl biotypeprotein_coding
OMIM610495
Entrez25900

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000336604, ENST00000356896, ENST00000396830, ENST00000396840, ENST00000465801, ENST00000471408, ENST00000472558, ENST00000487279, ENST00000488007, ENST00000619571, ENST00000900775, ENST00000900776, ENST00000952552, ENST00000952553

RefSeq mRNA: 5 — MANE Select: NM_001193457 NM_001039670, NM_001193457, NM_001330324, NM_001330325, NM_080730

CCDS: CCDS41741, CCDS73425, CCDS81655, CCDS8550

Canonical transcript exons

ENST00000619571 — 10 exons

ExonStartEnd
ENSE0000170092165395396540588
ENSE0000180327765494766549484
ENSE0000348108965484256548545
ENSE0000359064965506956550790
ENSE0000362690565415126541642
ENSE0000362969965497566549896
ENSE0000363729665509416551001
ENSE0000365237465480656548160
ENSE0000373163865486686548849
ENSE0000373583765552576556042

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 96.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.4651 / max 189.0299, expressed in 1558 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
12911815.11231504
1291125.1151811
1291170.9980575
1291140.443090
1291130.3630147
1291090.3564226
1291160.077434

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tendon of biceps brachiiUBERON:000818896.26gold quality
granulocyteCL:000009496.04gold quality
right coronary arteryUBERON:000162594.96gold quality
apex of heartUBERON:000209894.28gold quality
right hemisphere of cerebellumUBERON:001489093.93gold quality
spleenUBERON:000210693.85gold quality
descending thoracic aortaUBERON:000234593.81gold quality
cerebellar hemisphereUBERON:000224593.47gold quality
cerebellar cortexUBERON:000212993.31gold quality
thoracic aortaUBERON:000151593.17gold quality
ascending aortaUBERON:000149693.12gold quality
right frontal lobeUBERON:000281093.12gold quality
monocyteCL:000057692.88gold quality
body of uterusUBERON:000985392.88gold quality
left uterine tubeUBERON:000130392.80gold quality
mononuclear cellCL:000084292.78gold quality
left coronary arteryUBERON:000162692.32gold quality
leukocyteCL:000073892.26gold quality
mucosa of stomachUBERON:000119992.25gold quality
cerebellumUBERON:000203792.12gold quality
coronary arteryUBERON:000162191.98gold quality
right adrenal gland cortexUBERON:003582791.90gold quality
tibial nerveUBERON:000132391.89gold quality
right ovaryUBERON:000211891.54gold quality
esophagogastric junction muscularis propriaUBERON:003584191.51gold quality
aortaUBERON:000094791.47gold quality
right adrenal glandUBERON:000123391.45gold quality
left adrenal gland cortexUBERON:003582591.31gold quality
lower esophagus muscularis layerUBERON:003583391.05gold quality
stromal cell of endometriumCL:000225591.02gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting IFFO1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4510100.0066.602050
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-126-5P100.0072.713180
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-568299.8972.561005
HSA-MIR-7845-5P99.8864.88771
HSA-MIR-6848-3P99.6466.49885
HSA-MIR-766-5P99.4767.912225
HSA-MIR-766-3P99.4765.241811
HSA-MIR-6843-3P99.2666.42915
HSA-MIR-429399.2265.461263
HSA-MIR-6510-5P99.1466.591081
HSA-MIR-6868-5P99.0665.691284
HSA-MIR-211-3P98.1466.771052
HSA-MIR-3190-3P97.6166.951406
HSA-MIR-1225-3P97.2964.60876
HSA-MIR-874-5P96.9363.921014
HSA-MIR-432393.9363.89656
HSA-MIR-444292.3567.0898

Literature-anchored findings (GeneRIF, showing 3)

  • The lamin A/C-IFFO1-constituted nucleoskeleton prevents chromosome translocation by immobilizing broken DNA ends during tumorigenesis. (PMID:31548606)
  • METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance. (PMID:36257380)
  • CircIFFO1 suppresses tumor growth and metastasis of cutaneous squamous cell carcinoma by targeting the miR-424-5p/NFIB axis. (PMID:37405427)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioiffo1bENSDARG00000062108
danio_rerioiffo1aENSDARG00000062976
mus_musculusIffo1ENSMUSG00000038271
rattus_norvegicusIffo1ENSRNOG00000018533

Paralogs (1): IFFO2 (ENSG00000169991)

Protein

Protein identifiers

Non-homologous end joining factor IFFO1Q0D2I5 (reviewed: Q0D2I5)

Alternative names: Intermediate filament family orphan 1, Tumor antigen HOM-TES-103

All UniProt accessions (3): Q0D2I5, A0A087WZ16, E9PPX7

UniProt curated annotations — full annotation on UniProt →

Function. Nuclear matrix protein involved in the immobilization of broken DNA ends and the suppression of chromosome translocation during DNA double-strand breaks (DSBs). Interacts with the nuclear lamina component LMNA, resulting in the formation of a nucleoskeleton that relocalizes to the DSB sites in a XRCC4-dependent manner and promotes the immobilization of the broken ends, thereby preventing chromosome translocation. Acts as a scaffold that allows the DNA repair protein XRCC4 and LMNA to assemble into a complex at the DSB sites.

Subunit / interactions. Forms a heterotetramer with XRCC4. The interaction with XRCC4 is direct, involves LIG4-free XRCC4 and leads to relocalization of IFFO1 at the double-strand break (DSB) sites. Interacts with LMNA; the interaction forms an interior nucleoskeleton and the recruitment to DNA double-strand breaks.

Subcellular location. Nucleus. Nucleoplasm. Nucleus inner membrane. Nucleus matrix.

Tissue specificity. Ubiquitously expressed.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the intermediate filament family.

Isoforms (7)

UniProt IDNamesCanonical?
Q0D2I5-11yes
Q0D2I5-22
Q0D2I5-33
Q0D2I5-44
Q0D2I5-55
Q0D2I5-66
Q0D2I5-77

RefSeq proteins (5): NP_001034759, NP_001180386, NP_001317253, NP_001317254, NP_542768 (=MANE)

Domains & families (InterPro)

IDNameType
IPR039008IF_rod_domDomain

UniProt features (39 total): mutagenesis site 12, splice variant 6, region of interest 6, sequence conflict 6, coiled-coil region 3, compositionally biased region 2, helix 2, chain 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6ABOX-RAY DIFFRACTION2.65

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q0D2I5-F167.530.33

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 (12):

PositionPhenotype
65does not affect the interaction with lmna.
73decreased interaction with lmna. loss of ability to immobilize broken ends; when associated with h-85.
73does not affect the interaction with lmna.
85decreased interaction with lmna.
89does not affect the interaction with lmna.
480loss of interaction with xrcc4; when associated with r-487.
487loss of interaction with xrcc4; when associated with r-480.
490decreased interaction with xrcc4; when associated with a-516. loss of interaction with xrcc4; when associated with a-509
509loss of interaction with xrcc4; when associated with a-490 and a-516.
512loss of interaction with xrcc4.
515loss of interaction with xrcc4, loss of localization at the sites of dna damages and loss of ability to immobilize broke
516decreased interaction with xrcc4; when associated with a-490. loss of interaction with xrcc4; when associated with a-490

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 189 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, SHEPARD_CRASH_AND_BURN_MUTANT_UP, MODULE_45, GOBP_CHROMOSOME_LOCALIZATION, TGACCTY_ERR1_Q2, BOYLAN_MULTIPLE_MYELOMA_D_DN, TTGGGAG_MIR150, COUP_01, CAGCAGG_MIR370, ONKEN_UVEAL_MELANOMA_UP, GOBP_PROTEIN_LOCALIZATION_TO_CHROMOSOME, HNF4_DR1_Q3, GOBP_DNA_DAMAGE_RESPONSE, HNF4_01, PPAR_DR1_Q2

GO Biological Process (3): double-strand break repair via nonhomologous end joining (GO:0006303), protein localization to site of double-strand break (GO:1990166), DNA double-strand break attachment to nuclear envelope (GO:1990683)

GO Molecular Function (2): cytoskeletal adaptor activity (GO:0008093), protein binding (GO:0005515)

GO Cellular Component (7): nuclear inner membrane (GO:0005637), nucleoplasm (GO:0005654), intermediate filament (GO:0005882), nuclear matrix (GO:0016363), site of double-strand break (GO:0035861), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
nuclear lumen2
double-strand break repair1
protein localization to chromosome1
chromosome attachment to the nuclear envelope1
cytoskeletal protein binding1
protein-macromolecule adaptor activity1
binding1
organelle inner membrane1
nuclear membrane1
intermediate filament cytoskeleton1
polymeric cytoskeletal fiber1
site of DNA damage1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

410 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
IFFO1XRCC4Q13426771
IFFO1XRCC6P12956552
IFFO1XRCC5P13010518
IFFO1MARCHF9Q86YJ5441
IFFO1NEK11Q8NG66415
IFFO1NHEJ1Q9H9Q4414
IFFO1C11orf52Q96A22396
IFFO1PAXXQ9BUH6392
IFFO1JMJD8Q96S16376
IFFO1CYRENQ9BWK5374
IFFO1HID1Q8IV36370
IFFO1LIG4P49917370
IFFO1C5orf22Q49AR2368
IFFO1NEK9Q8TD19354
IFFO1AIRIMQ9NX04351

IntAct

57 interactions, top by confidence:

ABTypeScore
XRCC4LIG4psi-mi:“MI:0914”(association)0.970
XRCC4IFFO1psi-mi:“MI:0915”(physical association)0.820
SNX32SNX2psi-mi:“MI:0914”(association)0.740
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
NHEJ1XRCC5psi-mi:“MI:0914”(association)0.710
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
PPP1R13BCCDC85Cpsi-mi:“MI:0914”(association)0.530
ZNF331USP9Ypsi-mi:“MI:0914”(association)0.530
XRCC4NFKB1psi-mi:“MI:0914”(association)0.530
COG5BSGpsi-mi:“MI:0914”(association)0.530
LMNAIFFO1psi-mi:“MI:0914”(association)0.500
IFFO1LMNApsi-mi:“MI:0915”(physical association)0.500
IFFO1LMNApsi-mi:“MI:0915”(physical association)0.400
LIG4XRCC5psi-mi:“MI:0915”(physical association)0.400
IFFO1XRCC5psi-mi:“MI:0915”(physical association)0.400
IFFO1RNF183psi-mi:“MI:0915”(physical association)0.370
ACAP1IFFO1psi-mi:“MI:0915”(physical association)0.370
EGLN3FAM168Bpsi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
repVWA8psi-mi:“MI:0914”(association)0.350
KRT2IFT56psi-mi:“MI:0914”(association)0.350
FAM167ASHTN1psi-mi:“MI:0914”(association)0.350
MAGEA9CIBAR1psi-mi:“MI:0914”(association)0.350

BioGRID (74): IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), IFFO1 (Two-hybrid), RNF183 (Two-hybrid), IFFO1 (Two-hybrid), TCHP (Two-hybrid), IFFO1 (Reconstituted Complex), IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS)

ESM2 similar proteins: A0A088MLT8, A2AQ25, B3KU38, B5DF41, E9PSK7, O15079, O35274, P0DPB3, P0DPB4, P12755, P49140, P85299, Q0D2I5, Q14DQ1, Q1LY51, Q3B7M3, Q3SYW5, Q4KMA0, Q4R3X1, Q50H33, Q5F3L9, Q5FVG6, Q5RD40, Q5XKK7, Q60698, Q6ZNC4, Q6ZUS6, Q6ZWB6, Q80U23, Q80U62, Q80XA6, Q812A5, Q86YI8, Q8BXL9, Q8K2W6, Q8ND83, Q8NFH8, Q8QFX1, Q8TEK3, Q924W7

Diamond homologs: A5A6M8, A6QNX5, O77788, O93532, P02542, P05786, P05787, P07196, P07197, P08552, P08553, P08776, P08777, P0C6R4, P11679, P12839, P13647, P16053, P16878, P23565, P46660, P48671, P48677, P54938, Q02916, Q08DH7, Q0D2I5, Q16352, Q5R408, Q5RA72, Q5TF58, Q5XKE5, Q5XQN5, Q6IG12, Q6P6Q2, Q6PVZ1, Q8BXL9, Q8R2V2, Q922U2, Q9DCV7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 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:

PathwayPartnersFoldFDR
Formation of the cornified envelope614.2×3e-04
Keratinization69.0×3e-03

GO biological processes:

GO termPartnersFoldFDR
double-strand break repair via nonhomologous end joining537.0×4e-05
intermediate filament organization729.6×1e-06
keratinization520.5×4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance91
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1646 predictions. Top by Δscore:

VariantEffectΔscore
12:6540585:CTTT:Cacceptor_gain1.0000
12:6541507:CCTA:Cdonor_loss1.0000
12:6541508:CTAC:Cdonor_loss1.0000
12:6541509:TACC:Tdonor_loss1.0000
12:6541510:A:Tdonor_loss1.0000
12:6541511:CCGGT:Cdonor_gain1.0000
12:6541639:CCAG:Cacceptor_gain1.0000
12:6541640:CAG:Cacceptor_gain1.0000
12:6541640:CAGC:Cacceptor_gain1.0000
12:6541643:C:CCacceptor_gain1.0000
12:6548059:CCTTA:Cdonor_loss1.0000
12:6548060:CTTA:Cdonor_loss1.0000
12:6548061:TTA:Tdonor_loss1.0000
12:6548062:TA:Tdonor_loss1.0000
12:6548063:ACCTC:Adonor_loss1.0000
12:6548064:C:Gdonor_loss1.0000
12:6548457:AG:Adonor_gain1.0000
12:6548617:T:TAdonor_gain1.0000
12:6548666:A:ACdonor_gain1.0000
12:6548667:C:CCdonor_gain1.0000
12:6548667:CAG:Cdonor_gain1.0000
12:6549752:TCA:Tdonor_loss1.0000
12:6549753:CAC:Cdonor_loss1.0000
12:6549754:A:ACdonor_gain1.0000
12:6549755:C:CCdonor_gain1.0000
12:6549897:C:CCacceptor_gain1.0000
12:6549902:C:CTacceptor_gain1.0000
12:6549902:C:Tacceptor_gain1.0000
12:6549903:A:Tacceptor_gain1.0000
12:6549911:C:CTacceptor_gain1.0000

AlphaMissense

3709 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:6541533:A:GL518P1.000
12:6541536:C:GR517P1.000
12:6541539:C:GR516P1.000
12:6541543:A:GC515R1.000
12:6541551:A:GM512T1.000
12:6541561:C:GD509H1.000
12:6541563:A:GL508P1.000
12:6541563:A:TL508Q1.000
12:6541567:C:GG507R1.000
12:6541569:C:GR506P1.000
12:6541570:G:TR506S1.000
12:6541571:C:AK505N1.000
12:6541571:C:GK505N1.000
12:6541573:T:CK505E1.000
12:6541577:G:CS503R1.000
12:6541577:G:TS503R1.000
12:6541579:T:GS503R1.000
12:6541580:G:CC502W1.000
12:6541581:C:TC502Y1.000
12:6541582:A:GC502R1.000
12:6541583:C:AM501I1.000
12:6541583:C:GM501I1.000
12:6541583:C:TM501I1.000
12:6541584:A:CM501R1.000
12:6541584:A:GM501T1.000
12:6541593:T:CY498C1.000
12:6541594:A:GY498H1.000
12:6541602:A:GL495P1.000
12:6541602:A:TL495Q1.000
12:6541605:T:GH494P1.000

dbSNP variants (sampled 300 via entrez): RS1000043749 (12:6545838 G>A), RS1000108220 (12:6543285 G>A,C), RS1000335740 (12:6553504 C>G), RS1000398238 (12:6556824 T>TA), RS1000453804 (12:6553332 A>T), RS1000495382 (12:6541927 T>C), RS1000561343 (12:6550020 C>T), RS1000626349 (12:6551241 T>A), RS1000647946 (12:6546839 C>G), RS1000744627 (12:6555942 C>A), RS1001016943 (12:6550185 C>T), RS1001439727 (12:6538703 A>G), RS1001505905 (12:6543801 A>C), RS1001754507 (12:6538862 G>A,C), RS1001787041 (12:6541064 G>A,C)

Disease associations

OMIM: gene MIM:610495 | 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):

StudyTraitp-value
GCST008159_50Waist-to-hip ratio adjusted for BMI3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
arseniteincreases methylation1
mono-(2-ethylhexyl)phthalateincreases abundance, increases methylation1
2-amino-9H-pyrido(2,3-b)indoledecreases expression1
sodium arseniteincreases expression1
tobacco tardecreases reaction, increases expression1
diallyl disulfidedecreases reaction, increases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
beta-methylcholineaffects expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
jinfukangincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation, decreases methylation1
Calcitrioldecreases expression1
Diethylhexyl Phthalateincreases methylation, increases abundance1
Doxorubicinincreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Methyl Methanesulfonateincreases expression1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Vitamin Eincreases expression1
Aflatoxin B1decreases expression1
Copper Sulfatedecreases expression1
Particulate Matterincreases abundance, decreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.