IFFO2

Summary

IFFO2 (intermediate filament family orphan 2, HGNC:27006) is a protein-coding gene on chromosome 1p36.13, encoding Intermediate filament family orphan 2 (Q5TF58).

Predicted to be located in intermediate filament.

Source: NCBI Gene 126917 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 86 total
• MANE Select transcript: NM_001136265

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27006
Approved symbol	IFFO2
Name	intermediate filament family orphan 2
Location	1p36.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000169991
Ensembl biotype	protein_coding
Entrez	126917

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000355609, ENST00000416166, ENST00000455833, ENST00000944819

RefSeq mRNA: 1 — MANE Select: NM_001136265 NM_001136265

CCDS: CCDS44076

Canonical transcript exons

ENST00000455833 — 9 exons

Exon	Start	End
ENSE00001704033	18955668	18956676
ENSE00003980694	18904280	18908666
ENSE00003980695	18911384	18911476
ENSE00003980697	18916903	18917042
ENSE00003980700	18919678	18919773
ENSE00003980704	18918362	18918502
ENSE00003980705	18911963	18912083
ENSE00003980706	18921061	18921121
ENSE00003980707	18910342	18910472

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 99.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1545 / max 397.6504, expressed in 1657 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
10622	7.4920	1433
10624	2.8434	1337
10623	0.7174	342
10621	0.1018	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	99.46	gold quality
skin of leg	UBERON:0001511	97.55	gold quality
zone of skin	UBERON:0000014	97.14	gold quality
skin of abdomen	UBERON:0001416	97.12	gold quality
upper leg skin	UBERON:0004262	95.55	gold quality
gingival epithelium	UBERON:0001949	95.35	gold quality
gingiva	UBERON:0001828	95.19	gold quality
nipple	UBERON:0002030	93.32	gold quality
skin of hip	UBERON:0001554	91.06	gold quality
mammalian vulva	UBERON:0000997	90.10	gold quality
lower esophagus mucosa	UBERON:0035834	89.68	gold quality
cerebellar vermis	UBERON:0004720	89.01	gold quality
esophagus mucosa	UBERON:0002469	88.36	gold quality
pharyngeal mucosa	UBERON:0000355	88.17	gold quality
cerebellar cortex	UBERON:0002129	87.61	gold quality
cerebellar hemisphere	UBERON:0002245	87.57	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.56	gold quality
cerebellum	UBERON:0002037	87.16	gold quality
penis	UBERON:0000989	86.95	gold quality
esophagus squamous epithelium	UBERON:0006920	85.48	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	85.47	gold quality
epithelium of mammary gland	UBERON:0003244	84.55	silver quality
mammary duct	UBERON:0001765	84.52	silver quality
mucosa of paranasal sinus	UBERON:0005030	84.29	silver quality
body of pancreas	UBERON:0001150	83.83	gold quality
granulocyte	CL:0000094	83.73	gold quality
esophagus	UBERON:0001043	83.54	gold quality
body of tongue	UBERON:0011876	83.54	gold quality
pancreas	UBERON:0001264	83.22	gold quality
mouth mucosa	UBERON:0003729	82.94	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

253 targeting IFFO2, 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-6867-5P	100.00	82.21	3464
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-340-5P	100.00	72.50	4437
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-4476	100.00	68.18	2030
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-8068	99.98	73.85	2376

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	iffo2a	ENSDARG00000062101
danio_rerio	iffo2b	ENSDARG00000102911
mus_musculus	Iffo2	ENSMUSG00000041025
rattus_norvegicus	Iffo2	ENSRNOG00000071266

Paralogs (1): IFFO1 (ENSG00000010295)

Protein

Protein identifiers

Intermediate filament family orphan 2 — Q5TF58 (reviewed: Q5TF58)

All UniProt accessions (3): Q5TF58, H0Y4W3, J3KNZ4

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the intermediate filament family.

RefSeq proteins (1): NP_001129737* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039008	IF_rod_dom	Domain

Pfam: PF00038

UniProt features (7 total): region of interest 3, compositionally biased region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TF58-F1	69.78	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 152 (showing top): SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, MARTINEZ_RB1_TARGETS_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP, SANSOM_APC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, DODD_NASOPHARYNGEAL_CARCINOMA_DN, chr1p36, FEVR_CTNNB1_TARGETS_DN, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP, DELACROIX_RARG_BOUND_MEF, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): intermediate filament (GO:0005882)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intermediate filament cytoskeleton	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

380 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFFO2	SMIM15	Q7Z3B0	447
IFFO2	ITSN1	Q15811	438
IFFO2	DESI2	Q9BSY9	437
IFFO2	WDR75	Q8IWA0	409
IFFO2	HSDL1	Q3SXM5	397
IFFO2	SEC22C	Q9BRL7	393
IFFO2	KPNA4	O00629	390
IFFO2	ARMC7	Q9H6L4	386
IFFO2	NSA2	O95478	384
IFFO2	EPHA4	P54764	371
IFFO2	FOXK2	Q01167	371
IFFO2	POF1B	Q8WVV4	371
IFFO2	CGN	Q9P2M7	353
IFFO2	ITPK1	Q13572	348
IFFO2	CASTOR2	A6NHX0	347

IntAct

25 interactions, top by confidence:

A	B	Type	Score
XRCC4	LIG4	psi-mi:“MI:0914”(association)	0.970
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
ATP5PF	ATP5PD	psi-mi:“MI:0914”(association)	0.670
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
IFT57	IFT56	psi-mi:“MI:0914”(association)	0.640
PPP1R13B	CCDC85C	psi-mi:“MI:0914”(association)	0.530
XRCC4	NFKB1	psi-mi:“MI:0914”(association)	0.530
Dynll1		psi-mi:“MI:0915”(physical association)	0.400
FGFR2	U2SURP	psi-mi:“MI:0914”(association)	0.350
XRCC4	NFKB1	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
LURAP1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
MAGEA9	CIBAR1	psi-mi:“MI:0914”(association)	0.350
CFAP184	TARS3	psi-mi:“MI:0914”(association)	0.350
P4HA2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SCCPDH	IPO5	psi-mi:“MI:0914”(association)	0.350
WDR83	ISY1-RAB43	psi-mi:“MI:0914”(association)	0.350
XRCC4	HLA-G	psi-mi:“MI:0914”(association)	0.350

BioGRID (25): IFFO2 (Affinity Capture-MS), IFFO2 (Affinity Capture-MS), IFFO2 (Affinity Capture-MS), IFFO2 (Proximity Label-MS), IFFO2 (Affinity Capture-RNA), IFFO2 (Proximity Label-MS), IFFO2 (Proximity Label-MS), IFFO2 (Affinity Capture-RNA), IFFO2 (Proximity Label-MS), IFFO2 (Proximity Label-MS), IFFO2 (Affinity Capture-MS), IFFO2 (Affinity Capture-MS), IFFO2 (Affinity Capture-MS), IFFO2 (Affinity Capture-MS), IFFO2 (Affinity Capture-MS)

ESM2 similar proteins: A0PJP4, B7ZAP0, E9PSK7, O60271, O88447, P0C6R4, P37285, P83094, Q07866, Q0VCP9, Q14161, Q17QG3, Q28623, Q2QLI6, Q3KR37, Q4V328, Q5EA89, Q5EBL4, Q5FVJ0, Q5HYJ3, Q5R4V2, Q5R581, Q5R9B3, Q5TF58, Q5ZJ65, Q66H91, Q6P643, Q6PBM7, Q6Z746, Q7L099, Q7Z3E2, Q80XP8, Q80YA9, Q8BR07, Q8C9S4, Q8R2V2, Q8TAV0, Q8TD16, Q8VD04, Q8WXI2

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	79
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1360 predictions. Top by Δscore:

Variant	Effect	Δscore
1:18910337:GGTA:G	donor_loss	1.0000
1:18910338:GTAC:G	donor_loss	1.0000
1:18910338:GTACC:G	donor_loss	1.0000
1:18910339:TAC:T	donor_loss	1.0000
1:18910339:TACC:T	donor_loss	1.0000
1:18910340:A:C	donor_loss	1.0000
1:18910340:A:T	donor_loss	1.0000
1:18910341:C:A	donor_loss	1.0000
1:18910341:C:CG	donor_loss	1.0000
1:18910341:CCTGT:C	donor_gain	1.0000
1:18910468:TCGA:T	acceptor_gain	1.0000
1:18910468:TCGAG:T	acceptor_gain	1.0000
1:18910469:CGAG:C	acceptor_gain	1.0000
1:18910469:CGAGC:C	acceptor_gain	1.0000
1:18910470:GAG:G	acceptor_gain	1.0000
1:18910471:AG:A	acceptor_gain	1.0000
1:18910471:AGCT:A	acceptor_loss	1.0000
1:18910472:GCTG:G	acceptor_loss	1.0000
1:18910473:C:CA	acceptor_loss	1.0000
1:18910473:C:CC	acceptor_gain	1.0000
1:18910473:CTGGG:C	acceptor_loss	1.0000
1:18910474:T:A	acceptor_loss	1.0000
1:18910483:CCAA:C	acceptor_gain	1.0000
1:18910484:C:CT	acceptor_gain	1.0000
1:18910484:C:T	acceptor_gain	1.0000
1:18910484:CAA:C	acceptor_gain	1.0000
1:18910485:A:T	acceptor_gain	1.0000
1:18910486:A:AC	acceptor_gain	1.0000
1:18910486:A:C	acceptor_gain	1.0000
1:18911380:TCA:T	donor_loss	1.0000

AlphaMissense

3419 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:18910363:A:G	L476P	1.000
1:18910369:C:G	R474P	1.000
1:18910373:A:G	C473R	1.000
1:18910381:A:G	M470T	1.000
1:18910384:T:G	Q469P	1.000
1:18910391:C:G	D467H	1.000
1:18910393:A:C	L466R	1.000
1:18910393:A:G	L466P	1.000
1:18910393:A:T	L466Q	1.000
1:18910396:C:T	G465D	1.000
1:18910397:C:G	G465R	1.000
1:18910399:C:G	R464P	1.000
1:18910401:C:A	K463N	1.000
1:18910401:C:G	K463N	1.000
1:18910403:T:C	K463E	1.000
1:18910407:G:C	S461R	1.000
1:18910407:G:T	S461R	1.000
1:18910409:T:G	S461R	1.000
1:18910410:G:C	C460W	1.000
1:18910411:C:T	C460Y	1.000
1:18910412:A:G	C460R	1.000
1:18910414:A:C	M459R	1.000
1:18910414:A:G	M459T	1.000
1:18910414:A:T	M459K	1.000
1:18910423:T:C	Y456C	1.000
1:18910424:A:G	Y456H	1.000
1:18910432:A:G	L453P	1.000
1:18910435:T:G	H452P	1.000
1:18910436:G:C	H452D	1.000
1:18910438:C:G	R451P	1.000

dbSNP variants (sampled 300 via entrez): RS1000081390 (1:18924853 G>A), RS1000190922 (1:18949035 G>A), RS1000196463 (1:18955887 G>A), RS1000244050 (1:18943013 C>A,T), RS1000249566 (1:18916197 G>C), RS1000296319 (1:18943233 G>T), RS1000438747 (1:18911561 C>T), RS1000469830 (1:18926631 G>A), RS1000535276 (1:18915211 G>A), RS1000576552 (1:18944149 G>A), RS1000597312 (1:18907249 C>A,T), RS1000630272 (1:18944458 G>A), RS1000658550 (1:18956627 G>A), RS1000664059 (1:18906028 C>T), RS1000698052 (1:18912681 C>T)

Disease associations

OMIM: gene `` | 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
Estradiol	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Valproic Acid	increases expression, increases methylation	2
aristolochic acid I	decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
sodium arsenate	increases abundance, decreases expression	1
trichostatin A	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants, Occupational	increases expression	1
Arsenic	decreases expression, increases abundance	1
Carbamazepine	affects expression	1
Demecolcine	increases expression	1

Clinical trials (associated diseases)

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