FDXACB1

Summary

FDXACB1 (ferredoxin-fold anticodon binding domain containing 1, HGNC:25110) is a protein-coding gene on chromosome 11q23.1, encoding Ferredoxin-fold anticodon-binding domain-containing protein 1 (Q9BRP7).

This gene encodes a protein which contains a ferredoxin-fold anticodon-binding domain which is contained in a subset of phenylalanyl tRNA synthetases. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 91893 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 104 total
• MANE Select transcript: NM_138378

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25110
Approved symbol	FDXACB1
Name	ferredoxin-fold anticodon binding domain containing 1
Location	11q23.1
Locus type	gene with protein product
Status	Approved
Aliases	LOC91893, hCG_2033039
Ensembl gene	ENSG00000255561
Ensembl biotype	protein_coding
Entrez	91893

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000260257, ENST00000528274, ENST00000531487, ENST00000866429

RefSeq mRNA: 1 — MANE Select: NM_138378 NM_138378

CCDS: CCDS44729

Canonical transcript exons

ENST00000260257 — 5 exons

Exon	Start	End
ENSE00000930517	111874056	111876104
ENSE00002144811	111878961	111879165
ENSE00003528383	111878556	111878712
ENSE00003529791	111876808	111877011
ENSE00003749000	111876481	111876639

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 83.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.3433 / max 30.1615, expressed in 1236 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122279	2.0536	1139
122278	0.2897	152

Top tissues by expression

258 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	83.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.92	gold quality
islet of Langerhans	UBERON:0000006	74.86	gold quality
ileal mucosa	UBERON:0000331	74.83	silver quality
cortical plate	UBERON:0005343	73.42	gold quality
ventricular zone	UBERON:0003053	72.73	gold quality
granulocyte	CL:0000094	71.74	gold quality
sperm	CL:0000019	71.42	silver quality
ganglionic eminence	UBERON:0004023	71.32	gold quality
embryo	UBERON:0000922	71.31	gold quality
right adrenal gland	UBERON:0001233	70.66	gold quality
right adrenal gland cortex	UBERON:0035827	70.23	gold quality
left adrenal gland	UBERON:0001234	69.45	gold quality
leukocyte	CL:0000738	68.91	gold quality
left adrenal gland cortex	UBERON:0035825	68.78	gold quality
monocyte	CL:0000576	68.44	gold quality
vermiform appendix	UBERON:0001154	68.41	gold quality
smooth muscle tissue	UBERON:0001135	67.88	gold quality
adrenal tissue	UBERON:0018303	67.83	gold quality
adrenal gland	UBERON:0002369	67.80	gold quality
right testis	UBERON:0004534	67.61	gold quality
rectum	UBERON:0001052	67.59	gold quality
pancreas	UBERON:0001264	67.36	gold quality
spleen	UBERON:0002106	67.27	gold quality
left testis	UBERON:0004533	67.25	gold quality
testis	UBERON:0000473	67.12	gold quality
adrenal cortex	UBERON:0001235	67.07	gold quality
stromal cell of endometrium	CL:0002255	66.97	gold quality
skin of abdomen	UBERON:0001416	66.87	gold quality
lymph node	UBERON:0000029	66.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting FDXACB1, 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-4668-3P	100.00	68.74	2635
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
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-652-5P	99.91	67.49	505
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-4284	99.36	65.25	1293
HSA-MIR-3973	99.20	69.19	1990
HSA-MIR-4528	99.18	69.77	1936
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-5587-5P	99.07	68.58	838
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-140-3P	99.04	67.69	1324
HSA-MIR-9500	98.62	66.54	1845
HSA-MIR-4722-5P	98.46	66.34	1611
HSA-MIR-340-3P	98.11	68.25	679

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	fdxacb1	ENSDARG00000095750
mus_musculus	Fdxacb1	ENSMUSG00000037845

Paralogs (2): FARS2 (ENSG00000145982), FARSA (ENSG00000179115)

Protein

Protein identifiers

Ferredoxin-fold anticodon-binding domain-containing protein 1 — Q9BRP7 (reviewed: Q9BRP7)

All UniProt accessions (3): Q9BRP7, B3KUL3, E9PK62

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BRP7-1	1	yes
Q9BRP7-2	2

RefSeq proteins (1): NP_612387* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005121	Fdx_antiC-bd	Domain
IPR019446	BMT5-like	Domain
IPR036690	Fdx_antiC-bd_sf	Homologous_superfamily
IPR045864	aa-tRNA-synth_II/BPL/LPL	Homologous_superfamily

Pfam: PF03147, PF10354

UniProt features (6 total): sequence variant 3, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRP7-F1	84.77	0.57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_RNA_METHYLATION, GOBP_RNA_MODIFICATION, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOBP_RRNA_MODIFICATION, GOBP_METHYLATION, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RRNA_METHYLATION, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_RNA_METHYLTRANSFERASE_ACTIVITY, GOMF_N_METHYLTRANSFERASE_ACTIVITY, GOMF_S_ADENOSYLMETHIONINE_DEPENDENT_METHYLTRANSFERASE_ACTIVITY, GSE13522_WT_VS_IFNG_KO_SKIN_DN, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_ONE_CARBON_GROUPS

GO Biological Process (1): rRNA base methylation (GO:0070475)

GO Molecular Function (2): rRNA (uridine-N3-)-methyltransferase activity (GO:0070042), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
rRNA methylation	1
N-methyltransferase activity	1
rRNA (uridine) methyltransferase activity	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2088 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FDXACB1	SLC23A3	Q6PIS1	404
FDXACB1	ATP8B3	O60423	393
FDXACB1	ARHGAP33	O14559	358
FDXACB1	LRRC1	Q9BTT6	358
FDXACB1	APMAP	Q9HDC9	353
FDXACB1	EPRS1	P07814	353
FDXACB1	YARS1	P54577	353
FDXACB1	PNPT1	Q8TCS8	353
FDXACB1	TRIT1	Q9H3H1	351
FDXACB1	RRP8	O43159	350
FDXACB1	SPOP	O43791	350
FDXACB1	ALDH18A1	P54886	350
FDXACB1	SPOPL	Q6IQ16	350
FDXACB1	TSR3	Q9UJK0	349
FDXACB1	WARS2	Q9UGM6	349
FDXACB1	VARS1	P26640	349
FDXACB1	EARS2	Q5JPH6	349

IntAct

26 interactions, top by confidence:

A	B	Type	Score
FDXACB1	TRAF2	psi-mi:“MI:0915”(physical association)	0.720
TRAF2	FDXACB1	psi-mi:“MI:0915”(physical association)	0.720
ZSCAN18	FDXACB1	psi-mi:“MI:0915”(physical association)	0.560
ZNF250	FDXACB1	psi-mi:“MI:0915”(physical association)	0.560
FDXACB1	TUBGCP4	psi-mi:“MI:0915”(physical association)	0.560
FDXACB1	MYNN	psi-mi:“MI:0915”(physical association)	0.560
THUMPD1	YBX1	psi-mi:“MI:0914”(association)	0.530
GALNT6	NDUFS4	psi-mi:“MI:0914”(association)	0.530
FDXACB1	H3-4	psi-mi:“MI:0915”(physical association)	0.400
FDXACB1	HERC4	psi-mi:“MI:0915”(physical association)	0.400
FDXACB1	HERC4	psi-mi:“MI:0914”(association)	0.350
FDXACB1	ZSCAN18	psi-mi:“MI:0915”(physical association)	0.000
FDXACB1	ZNF250	psi-mi:“MI:0915”(physical association)	0.000
FDXACB1	TUBGCP4	psi-mi:“MI:0915”(physical association)	0.000
FDXACB1	TRAF2	psi-mi:“MI:0915”(physical association)	0.000
FDXACB1	MYNN	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): FDXACB1 (Two-hybrid), FDXACB1 (Affinity Capture-MS), FDXACB1 (Affinity Capture-MS), HERC4 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), FDXACB1 (Two-hybrid), FDXACB1 (Two-hybrid), FDXACB1 (Two-hybrid), FDXACB1 (Two-hybrid), FDXACB1 (Two-hybrid), FDXACB1 (Proximity Label-MS), FDXACB1 (Affinity Capture-MS), FDXACB1 (Affinity Capture-MS), HERC4 (Affinity Capture-MS), PTPRF (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0JPF9, A4D126, A4D7T3, A4QNL8, A5PKL6, B2GUS6, C0IN03, E1BCH6, E1BVR9, F1LW30, F1ND48, P19686, P19687, P33402, P48760, P57075, Q02108, Q07DZ7, Q08C84, Q09M05, Q108U1, Q1L5Z9, Q1LZ50, Q28CZ7, Q32PY6, Q3U3W5, Q3UY23, Q4R3W5, Q4ZHS0, Q5REW9, Q5RG49, Q5RJG7, Q5RL51, Q5S6T3, Q5T8I9, Q6GPJ4, Q6NXP6, Q6P2P2, Q7SXA9, Q8BTK5

Diamond homologs: F4I1X0, O94480, P0C8L4, P40493, Q3UY23, Q9BRP7, A0M6W9, A3MJU2, A3MUA4, A3NUI8, A4FW27, A4JDU8, A4WHY5, A4XKJ8, A4YIL1, A5FLW1, A5IIW2, A6GVW9, A6LA92, A6VH81, A8Z6A5, A9B8B9, B0C6I2, B1LCK9, B1XYZ7, B2RLI5, B2S4L0, B2SZF8, B3ERN3, B3QUV1, B3R4J5, B4E7I9, B6YQ38, B6YTJ4, B9MRS9, C0R5D1, C5A5Y9, C5CUU6, C6A236, O16129

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1072 predictions. Top by Δscore:

Variant	Effect	Δscore
11:111876844:CAG:C	donor_gain	1.0000
11:111877007:CACAG:C	acceptor_gain	1.0000
11:111877009:CAG:C	acceptor_gain	1.0000
11:111877012:C:CC	acceptor_gain	1.0000
11:111878592:G:C	donor_gain	1.0000
11:111878955:CGCTA:C	donor_loss	1.0000
11:111878956:GCTAC:G	donor_loss	1.0000
11:111878957:CTACC:C	donor_loss	1.0000
11:111878958:TAC:T	donor_loss	1.0000
11:111878959:AC:A	donor_loss	1.0000
11:111878960:CCTCG:C	donor_gain	1.0000
11:111876102:CCC:C	acceptor_gain	0.9900
11:111876103:CCC:C	acceptor_gain	0.9900
11:111876899:C:CT	donor_gain	0.9900
11:111876904:TGCCA:T	donor_gain	0.9900
11:111876937:T:C	donor_gain	0.9900
11:111877008:ACAG:A	acceptor_gain	0.9900
11:111877009:CAGC:C	acceptor_gain	0.9900
11:111877010:AG:A	acceptor_gain	0.9900
11:111878550:CCTCA:C	donor_loss	0.9900
11:111878551:CTCAC:C	donor_loss	0.9900
11:111878552:TCACC:T	donor_loss	0.9900
11:111878553:CACCT:C	donor_loss	0.9900
11:111878554:A:AT	donor_loss	0.9900
11:111878554:A:C	donor_loss	0.9900
11:111878555:CCTT:C	donor_loss	0.9900
11:111878581:C:A	donor_gain	0.9900
11:111878909:TTGGG:T	donor_gain	0.9900
11:111878957:CTA:C	donor_loss	0.9900
11:111878958:TACCT:T	donor_loss	0.9900

AlphaMissense

4125 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:111875174:A:C	S541R	0.989
11:111875174:A:T	S541R	0.989
11:111875176:T:G	S541R	0.989
11:111876908:A:G	W145R	0.989
11:111876908:A:T	W145R	0.989
11:111876592:A:G	F194S	0.983
11:111876906:C:A	W145C	0.981
11:111876906:C:G	W145C	0.981
11:111875042:A:C	S585R	0.979
11:111875042:A:T	S585R	0.979
11:111875044:T:G	S585R	0.979
11:111876621:A:C	F184L	0.979
11:111876621:A:T	F184L	0.979
11:111876623:A:G	F184L	0.979
11:111876909:A:C	S144R	0.979
11:111876909:A:T	S144R	0.979
11:111876911:T:G	S144R	0.979
11:111875023:A:C	Y592D	0.978
11:111875121:G:T	A559D	0.977
11:111875035:A:C	Y588D	0.976
11:111875069:G:C	F576L	0.974
11:111875069:G:T	F576L	0.974
11:111875071:A:G	F576L	0.974
11:111875133:A:G	F555S	0.973
11:111875171:A:C	F542L	0.973
11:111875171:A:T	F542L	0.973
11:111875172:A:G	F542S	0.973
11:111875173:A:G	F542L	0.973
11:111878564:A:C	F107L	0.973
11:111878564:A:T	F107L	0.973

dbSNP variants (sampled 300 via entrez): RS1000043705 (11:111875242 C>A), RS1000266546 (11:111879973 G>T), RS1001322959 (11:111879458 G>C), RS1003034139 (11:111878610 C>G), RS1003391583 (11:111878245 G>C), RS1004446365 (11:111877910 G>A), RS1004782244 (11:111876505 T>C), RS1006241186 (11:111880384 G>C), RS1006353045 (11:111874646 T>G), RS1006385008 (11:111881023 C>A,T), RS1006744449 (11:111880593 A>G), RS1008122731 (11:111879217 T>A,C), RS1008255296 (11:111880261 C>G,T), RS1010203771 (11:111878322 C>T), RS1010582193 (11:111877312 T>C)

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

1 associations (top):

Study	Trait	p-value
GCST007564_5	Asthma or allergic disease (pleiotropy)	6.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Cisplatin	affects cotreatment, increases expression, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Calcitriol	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Oxygen	decreases expression	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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